Contents

1 Motivation & Introduction

The purpose of this package is to make it easy to query the Human Cell Atlas Data Portal via their data browser API. Visit the Human Cell Atlas for more information on the project.

1.1 Installation and getting started

Evaluate the following code chunk to install packages required for this vignette.

## install from Bioconductor if you haven't already
pkgs <- c("httr", "dplyr", "LoomExperiment", "hca")
pkgs_needed <- pkgs[!pkgs %in% rownames(installed.packages())]
BiocManager::install(pkgs_needed)

Load the packages into your R session.

library(httr)
library(dplyr)
library(LoomExperiment)
library(hca)

2 Example: Discover and download a ‘loom’ file

To illustrate use of this package, consider the task of downloading a ‘loom’ file summarizing single-cell gene expression observed in an HCA research project. This could be accomplished by visiting the HCA data portal (at https://data.humancellatlas.org/explore) in a web browser and selecting projects interactively, but it is valuable to accomplish the same goal in a reproducible, flexible, programmatic way. We will (1) discover projects available in the HCA Data Coordinating Center that have loom files; and (2) retrieve the file from the HCA and import the data into R as a ‘LoomExperiment’ object. For illustration, we focus on the ‘Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns’ project.

2.1 Discover projects with loom files

Use projects() to retrieve all projects in the HCA’s default catalog.

projects()
## # A tibble: 237 × 5
##    projectId             projectTitle genusSpecies samples.organ specimens.organ
##    <chr>                 <chr>        <list>       <list>        <list>         
##  1 74b6d569-3b11-42ef-b… 1.3 Million… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 53c53cd4-8127-4e12-b… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  4 60ea42e1-af49-42f5-8… A Protocol … <chr [1]>    <chr [1]>     <chr [1]>      
##  5 ef1e3497-515e-4bbe-8… A Single-Ce… <chr [1]>    <chr [3]>     <chr [3]>      
##  6 f86f1ab4-1fbb-4510-a… A Single-Ce… <chr [2]>    <chr [1]>     <chr [1]>      
##  7 602628d7-c038-48a8-a… A Single-ce… <chr [1]>    <chr [3]>     <chr [3]>      
##  8 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]>    <chr [2]>     <chr [2]>      
##  9 c0518445-3b3b-49c6-b… A cellular … <chr [1]>    <chr [2]>     <chr [2]>      
## 10 5116c081-8be7-49c5-8… A comprehen… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 227 more rows

Use filters() to restrict the projects to just those that contain at least one ‘loom’ file.

project_filter <- filters(fileFormat = list(is = "loom"))
project_tibble <- projects(project_filter)
project_tibble
## # A tibble: 79 × 5
##    projectId             projectTitle genusSpecies samples.organ specimens.organ
##    <chr>                 <chr>        <list>       <list>        <list>         
##  1 53c53cd4-8127-4e12-b… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  2 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]>    <chr [2]>     <chr [2]>      
##  4 a9301beb-e9fa-42fe-b… A human cel… <chr [1]>    <chr [14]>    <chr [14]>     
##  5 996120f9-e84f-409f-a… A human sin… <chr [1]>    <chr [1]>     <chr [1]>      
##  6 842605c7-375a-47c5-9… A single ce… <chr [1]>    <chr [1]>     <chr [1]>      
##  7 a004b150-1c36-4af6-9… A single-ce… <chr [1]>    <chr [1]>     <chr [1]>      
##  8 4a95101c-9ffc-4f30-a… A single-ce… <chr [1]>    <chr [4]>     <chr [4]>      
##  9 1cd1f41f-f81a-486b-a… A single-ce… <chr [1]>    <chr [1]>     <chr [1]>      
## 10 8185730f-4113-40d3-9… A single-ce… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 69 more rows

Use standard R commands to further filter projects to the one we are interested in, with title starting with “Single…”. Extract the unique projectId for this project.

project_tibble %>%
    filter(startsWith(projectTitle, "Single")) %>%
    t()
##                 [,1]                                               
## projectId       "0c3b7785-f74d-4091-8616-a68757e4c2a8"             
## projectTitle    "Single cell RNA sequencing of multiple myeloma II"
## genusSpecies    "Homo sapiens"                                     
## samples.organ   "hematopoietic system"                             
## specimens.organ "hematopoietic system"                             
##                 [,2]                                                                             
## projectId       "7b947aa2-43a7-4082-afff-222a3e3a4635"                                           
## projectTitle    "Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids"
## genusSpecies    character,2                                                                      
## samples.organ   "whole embryos"                                                                  
## specimens.organ character,2                                                                      
##                 [,3]                                                                                                             
## projectId       "99101928-d9b1-4aaf-b759-e97958ac7403"                                                                           
## projectTitle    "Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 dia" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "pancreas"                                                                                                       
## specimens.organ "pancreas"                                                                                                       
##                 [,4]                                                                     
## projectId       "520afa10-f9d2-4e93-ab7a-26c4c863ce18"                                   
## projectTitle    "Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)"
## genusSpecies    "Homo sapiens"                                                           
## samples.organ   "tonsil"                                                                 
## specimens.organ "tonsil"                                                                 
##                 [,5]                                                                                                             
## projectId       "23587fb3-1a4a-4f58-ad74-cc9a4cb4c254"                                                                           
## projectTitle    "Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hyb" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "liver"                                                                                                          
## specimens.organ "liver"                                                                                                          
##                 [,6]                                                                                                             
## projectId       "116965f3-f094-4769-9d28-ae675c1b569c"                                                                           
## projectTitle    "Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryon" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "embryo"                                                                                                         
## specimens.organ "embryo"                                                                                                         
##                 [,7]                                                                                                             
## projectId       "f6133d2a-9f3d-4ef9-9c19-c23d6c7e6cc0"                                                                           
## projectTitle    "Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypox" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   character,0                                                                                                      
## specimens.organ "breast"                                                                                                         
##                 [,8]                                                                                                             
## projectId       "cddab57b-6868-4be4-806f-395ed9dd635a"                                                                           
## projectTitle    "Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging an" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "pancreas"                                                                                                       
## specimens.organ "pancreas"                                                                                                       
##                 [,9]                                                                                                             
## projectId       "2d846095-8a33-4f3c-97d4-585bafac13b4"                                                                           
## projectTitle    "Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of huma" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "brain"                                                                                                          
## specimens.organ "brain"                                                                                                          
##                 [,10]                                                                                                            
## projectId       "e8808cc8-4ca0-4096-80f2-bba73600cba6"                                                                           
## projectTitle    "Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated" [truncated]
## genusSpecies    "Mus musculus"                                                                                                   
## samples.organ   character,3                                                                                                      
## specimens.organ character,3                                                                                                      
##                 [,11]                                                                                          
## projectId       "b51f49b4-0d2e-4cbd-bbd5-04cd171fc2fa"                                                         
## projectTitle    "Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue."
## genusSpecies    "Homo sapiens"                                                                                 
## samples.organ   "brain"                                                                                        
## specimens.organ "brain"                                                                                        
##                 [,12]                                              
## projectId       "2ef3655a-973d-4d69-9b41-21fa4041eed7"             
## projectTitle    "Single-cell RNA sequencing of normal human kidney"
## genusSpecies    "Homo sapiens"                                     
## samples.organ   "kidney"                                           
## specimens.organ "kidney"                                           
##                 [,13]                                                                                          
## projectId       "559bb888-7829-41f2-ace5-2c05c7eb81e9"                                                         
## projectTitle    "Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human."
## genusSpecies    "Homo sapiens"                                                                                 
## samples.organ   character,3                                                                                    
## specimens.organ character,3                                                                                    
##                 [,14]                                                                                      
## projectId       "4bec484d-ca7a-47b4-8d48-8830e06ad6db"                                                     
## projectTitle    "Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina"
## genusSpecies    "Homo sapiens"                                                                             
## samples.organ   "retina"                                                                                   
## specimens.organ "retina"                                                                                   
##                 [,15]                                                                                                            
## projectId       "2043c65a-1cf8-4828-a656-9e247d4e64f1"                                                                           
## projectTitle    "Single-cell RNA-seq analysis  throughout a 125-day differentiation protocol that converted H1 human" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   character,0                                                                                                      
## specimens.organ "embryo"                                                                                                         
##                 [,16]                                                                                                            
## projectId       "ae71be1d-ddd8-4feb-9bed-24c3ddb6e1ad"                                                                           
## projectTitle    "Single-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patient" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "pancreas"                                                                                                       
## specimens.organ "pancreas"                                                                                                       
##                 [,17]                                                    
## projectId       "f48e7c39-cc67-4055-9d79-bc437892840c"                   
## projectTitle    "Single-cell RNA-seq of human peripheral blood NKT cells"
## genusSpecies    "Homo sapiens"                                           
## samples.organ   "blood"                                                  
## specimens.organ "blood"                                                  
##                 [,18]                                                            
## projectId       "05be4f37-4506-429b-b112-506444507d62"                           
## projectTitle    "Single-cell RNA-seq reveals heterogeneity within human pre-cDCs"
## genusSpecies    "Homo sapiens"                                                   
## samples.organ   "blood"                                                          
## specimens.organ "blood"                                                          
##                 [,19]                                                                                                            
## projectId       "c1a9a93d-d9de-4e65-9619-a9cec1052eaa"                                                                           
## projectTitle    "Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineage" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "lung"                                                                                                           
## specimens.organ "lung"                                                                                                           
##                 [,20]                                                                                                            
## projectId       "07073c12-8006-4710-a00b-23abdb814904"                                                                           
## projectTitle    "Single-cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expressio" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "blood vessel"                                                                                                   
## specimens.organ "blood vessel"                                                                                                   
##                 [,21]                                                                                    
## projectId       "962bd805-eb89-4c54-bad2-008e497d1307"                                                   
## projectTitle    "Single-cell analysis reveals congruence between kidney organoids and human fetal kidney"
## genusSpecies    "Homo sapiens"                                                                           
## samples.organ   character,0                                                                              
## specimens.organ "skin of body"                                                                           
##                 [,22]                                                                                
## projectId       "1ce3b3dc-02f2-44a8-96da-d6d107b27a76"                                               
## projectTitle    "Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells"
## genusSpecies    "Homo sapiens"                                                                       
## samples.organ   "umbilical cord"                                                                     
## specimens.organ "umbilical cord"                                                                     
##                 [,23]                                                                                                            
## projectId       "ccd1f1ba-74ce-469b-9fc9-f6faea623358"                                                                           
## projectTitle    "Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health an" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "blood"                                                                                                          
## specimens.organ "blood"                                                                                                          
##                 [,24]                                                                                                            
## projectId       "5ee710d7-e2d5-4fe2-818d-15f5e31dae32"                                                                           
## projectTitle    "Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "lymph node"                                                                                                     
## specimens.organ "lymph node"                                                                                                     
##                 [,25]                                                                    
## projectId       "a39728aa-70a0-4201-b0a2-81b7badf3e71"                                   
## projectTitle    "Single-cell transcriptional profiles in human and mouse skeletal muscle"
## genusSpecies    character,2                                                              
## samples.organ   "skeletal muscle organ"                                                  
## specimens.organ "skeletal muscle organ"                                                  
##                 [,26]                                                                                        
## projectId       "78b2406d-bff2-46fc-8b61-20690e602227"                                                       
## projectTitle    "Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes"
## genusSpecies    "Homo sapiens"                                                                               
## samples.organ   "pancreas"                                                                                   
## specimens.organ "pancreas"                                                                                   
##                 [,27]                                                                                                            
## projectId       "2a72a4e5-66b2-405a-bb7c-1e463e8febb0"                                                                           
## projectTitle    "Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "hematopoietic system"                                                                                           
## specimens.organ "hematopoietic system"                                                                                           
##                 [,28]                                                                                                            
## projectId       "24c654a5-caa5-440a-8f02-582921f2db4a"                                                                           
## projectTitle    "Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation traj" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "eye"                                                                                                            
## specimens.organ "eye"                                                                                                            
##                 [,29]                                                                          
## projectId       "ce7b12ba-664f-4f79-8fc7-3de6b1892183"                                         
## projectTitle    "Single-nucleus RNA sequencing of human cortex affected by multiple sclerosis."
## genusSpecies    "Homo sapiens"                                                                 
## samples.organ   "brain"                                                                        
## specimens.organ "brain"

projectIds <-
    project_tibble %>%
    filter(startsWith(projectTitle, "Single")) %>%
    dplyr::pull(projectId)

projectId <- projectIds[1]

2.2 Discover and download the loom file of interest

files() retrieves (the first 1000) files from the Human Cell Atlas data portal. Construct a filter to restrict the files to loom files from the project we are interested in.

file_filter <- filters(
    projectId = list(is = projectId),
    fileFormat = list(is = "loom")
)

# only the two smallest files
file_tibble <- files(file_filter, size = 2, sort = "fileSize", order = "asc")

file_tibble
## # A tibble: 2 × 8
##   fileId            name  fileFormat   size version projectTitle projectId url  
##   <chr>             <chr> <chr>       <int> <chr>   <chr>        <chr>     <chr>
## 1 fe214fea-cc68-56… bone… loom       4.04e7 2021-0… Single cell… 0c3b7785… http…
## 2 3014ec47-1399-57… Bone… loom       6.35e7 2021-1… Single cell… 0c3b7785… http…

files_download() will download one or more files (one for each row) in file_tibble. The download is more complicated than simply following the url column of file_tibble, so it is not possible to simply copy the url into a browser. We’ll download the file and then immediately import it into R.

file_locations <- file_tibble %>% files_download()

LoomExperiment::import(unname(file_locations[1]),
                       type ="SingleCellLoomExperiment")
## class: SingleCellLoomExperiment 
## dim: 58347 3762 
## metadata(15): last_modified CreationDate ...
##   project.provenance.document_id specimen_from_organism.organ
## assays(1): matrix
## rownames: NULL
## rowData names(29): Gene antisense_reads ... reads_per_molecule
##   spliced_reads
## colnames: NULL
## colData names(43): CellID antisense_reads ... reads_unmapped
##   spliced_reads
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(0): NULL

Note that files_download() uses [BiocFileCache][https://bioconductor.org/packages/BiocFileCache], so individual files are only downloaded once.

3 Example: Illustrating access to h5ad files

This example walks through the process of file discovery and retrieval in a little more detail, using h5ad files created by the Python AnnData analysis software and available for some experiments in the default catalog.

3.1 Projects facets and terms

The first challenge is to understand what file formats are available from the HCA. Obtain a tibble describing the ‘facets’ of the data, the number of terms used in each facet, and the number of distinct values used to describe projects.

projects_facets()
## # A tibble: 35 × 3
##    facet              n_terms n_values
##    <chr>                <int>    <int>
##  1 assayType                1      237
##  2 biologicalSex            5      388
##  3 cellLineType             6      245
##  4 contactName           2225     2766
##  5 contentDescription      38      759
##  6 developmentStage       137      489
##  7 donorDisease           194      469
##  8 effectiveOrgan         114      416
##  9 fileFormat              50      767
## 10 fileSource              10      529
## # … with 25 more rows

Note the fileFormat facet, and repeat projects_facets() to discover detail about available file formats

projects_facets("fileFormat")
## # A tibble: 50 × 3
##    facet      term     count
##    <chr>      <chr>    <int>
##  1 fileFormat fastq.gz   198
##  2 fileFormat loom        79
##  3 fileFormat bam         77
##  4 fileFormat tar         47
##  5 fileFormat tsv.gz      41
##  6 fileFormat txt.gz      36
##  7 fileFormat mtx.gz      35
##  8 fileFormat csv         32
##  9 fileFormat bai         26
## 10 fileFormat csv.gz      26
## # … with 40 more rows

Note that there are 8 uses of the h5ad file format. Use this as a filter to discover relevant projects.

filters <- filters(fileFormat = list(is = "h5ad"))
projects(filters)
## # A tibble: 17 × 5
##    projectId             projectTitle genusSpecies samples.organ specimens.organ
##    <chr>                 <chr>        <list>       <list>        <list>         
##  1 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]>    <chr [2]>     <chr [2]>      
##  2 c0518445-3b3b-49c6-b… A cellular … <chr [1]>    <chr [2]>     <chr [2]>      
##  3 73769e0a-5fcd-41f4-9… A proximal-… <chr [1]>    <chr [2]>     <chr [2]>      
##  4 957261f7-2bd6-4358-a… A spatial m… <chr [1]>    <chr [1]>     <chr [1]>      
##  5 1dddae6e-3753-48af-b… Cell Types … <chr [1]>    <chr [1]>     <chr [2]>      
##  6 ad98d3cd-26fb-4ee3-9… Cells of th… <chr [1]>    <chr [1]>     <chr [1]>      
##  7 fde199d2-a841-4ed1-a… Cells of th… <chr [1]>    <chr [4]>     <chr [4]>      
##  8 83f5188e-3bf7-4956-9… Distinct mi… <chr [1]>    <chr [2]>     <chr [2]>      
##  9 2f676143-80c2-4bc6-b… Integrative… <chr [1]>    <chr [1]>     <chr [1]>      
## 10 c4077b3c-5c98-4d26-a… Ischaemic s… <chr [1]>    <chr [3]>     <chr [3]>      
## 11 091cf39b-01bc-42e5-9… Profiling o… <chr [1]>    <chr [0]>     <chr [1]>      
## 12 f83165c5-e2ea-4d15-a… Reconstruct… <chr [1]>    <chr [3]>     <chr [3]>      
## 13 31887183-a72c-4308-9… Single-nucl… <chr [1]>    <chr [7]>     <chr [7]>      
## 14 abe1a013-af7a-45ed-8… Spatio-temp… <chr [1]>    <chr [1]>     <chr [1]>      
## 15 b963bd4b-4bc1-4404-8… The cellula… <chr [1]>    <chr [1]>     <chr [1]>      
## 16 4e6f083b-5b9a-4393-9… The emergen… <chr [1]>    <chr [3]>     <chr [3]>      
## 17 455b46e6-d8ea-4611-8… Transcripto… <chr [1]>    <chr [3]>     <chr [3]>

3.2 Projects columns

The default tibble produced by projects() contains only some of the information available; the information is much richer.

To obtain a tibble with an expanded set of columns, you can specify that using the as parameter set to "tibble_expanded".

# an expanded set of columns for all or the first 4 projects
projects(as = 'tibble_expanded', size = 4)
## # A tibble: 4 × 102
##   projectId  cellSuspensions… cellSuspensions… cellSuspensions… cellSuspensions…
##   <chr>      <list>           <chr>            <list>                      <int>
## 1 74b6d569-… <chr [1]>        brain            <chr [1]>                 1330000
## 2 53c53cd4-… <chr [2]>        prostate gland   <chr [7]>                  108701
## 3 7027adc6-… <chr [0]>        heart            <chr [0]>                      NA
## 4 60ea42e1-… <chr [1]>        oral cavity      <chr [1]>                    1145
## # … with 97 more variables: dates.aggregateLastModifiedDate <chr>,
## #   dates.aggregateSubmissionDate <chr>, dates.aggregateUpdateDate <chr>,
## #   dates.lastModifiedDate <chr>, dates.submissionDate <chr>,
## #   dates.updateDate <chr>, donorOrganisms.biologicalSex <chr>,
## #   donorOrganisms.developmentStage <list>, donorOrganisms.disease <chr>,
## #   donorOrganisms.donorCount <int>, donorOrganisms.genusSpecies <chr>,
## #   donorOrganisms.id <list>, donorOrganisms.organismAgeRange.gte <list>, …

In the next sections, we’ll cover other options for the as parameter, and the data formats they return.

3.2.1 projects() as an R list

Instead of retrieving the result of projects() as a tibble, retrieve it as a ‘list-of-lists’

projects_list <- projects(as = "list")

This is a complicated structure. We will use lengths(), names(), and standard R list selection operations to navigate this a bit. At the top level there are three elements.

lengths(projects_list)
## pagination termFacets       hits 
##          8         36        237

hits represents each project as a list, e.g,.

lengths(projects_list$hits[[1]])
##         protocols           entryId           sources          projects 
##                 2                 1                 1                 1 
##           samples         specimens         cellLines    donorOrganisms 
##                 1                 1                 0                 1 
##         organoids   cellSuspensions             dates fileTypeSummaries 
##                 0                 1                 1                 2

shows that there are 10 different ways in which the first project is described. Each component is itself a list-of-lists, e.g.,

lengths(projects_list$hits[[1]]$projects[[1]])
##           projectId        projectTitle    projectShortname          laboratory 
##                   1                   1                   1                   1 
##  estimatedCellCount  projectDescription        contributors        publications 
##                   1                   1                   6                   1 
##  supplementaryLinks            matrices contributedAnalyses          accessions 
##                   1                   0                   1                   3 
##          accessible 
##                   1
projects_list$hits[[1]]$projects[[1]]$projectTitle
## [1] "1.3 Million Brain Cells from E18 Mice"

One can use standard R commands to navigate this data structure, and to, e.g., extract the projectTitle of each project.

3.2.2 projects() as an lol

Use as = "lol" to create a more convenient way to select, filter and extract elements from the list-of-lists by projects().

lol <- projects(as = "lol")
lol
## # class: lol_hca lol
## # number of distinct paths: 13155
## # total number of elements: 140994
## # number of leaf paths: 9736
## # number of leaf elements: 106055
## # lol_path():
## # A tibble: 13,155 × 3
##    path                                     n is_leaf
##    <chr>                                <int> <lgl>  
##  1 hits                                     1 FALSE  
##  2 hits[*]                                237 FALSE  
##  3 hits[*].cellLines                      237 FALSE  
##  4 hits[*].cellLines[*]                    39 FALSE  
##  5 hits[*].cellLines[*].cellLineType       39 FALSE  
##  6 hits[*].cellLines[*].cellLineType[*]    47 TRUE   
##  7 hits[*].cellLines[*].id                 39 FALSE  
##  8 hits[*].cellLines[*].id[*]             349 TRUE   
##  9 hits[*].cellLines[*].modelOrgan         39 FALSE  
## 10 hits[*].cellLines[*].modelOrgan[*]      47 TRUE   
## # … with 13,145 more rows

Use lol_select() to restrict the lol to particular paths, and lol_filter() to filter results to paths that are leafs, or with specific numbers of entries.

lol_select(lol, "hits[*].projects[*]")
## # class: lol_hca lol
## # number of distinct paths: 13031
## # total number of elements: 85334
## # number of leaf paths: 9678
## # number of leaf elements: 68199
## # lol_path():
## # A tibble: 13,031 × 3
##    path                                                                n is_leaf
##    <chr>                                                           <int> <lgl>  
##  1 hits[*].projects[*]                                               237 FALSE  
##  2 hits[*].projects[*].accessible                                    237 TRUE   
##  3 hits[*].projects[*].accessions                                    237 FALSE  
##  4 hits[*].projects[*].accessions[*]                                 640 FALSE  
##  5 hits[*].projects[*].accessions[*].accession                       640 TRUE   
##  6 hits[*].projects[*].accessions[*].namespace                       640 TRUE   
##  7 hits[*].projects[*].contributedAnalyses                           237 FALSE  
##  8 hits[*].projects[*].contributedAnalyses.developmentStage            4 FALSE  
##  9 hits[*].projects[*].contributedAnalyses.developmentStage.adult      4 FALSE  
## 10 hits[*].projects[*].contributedAnalyses.developmentStage.adult…     2 FALSE  
## # … with 13,021 more rows
lol_select(lol, "hits[*].projects[*]") |>
    lol_filter(n == 44, is_leaf)
## # class: lol_hca lol
## # number of distinct paths: 0
## # total number of elements: 0
## # number of leaf paths: 0
## # number of leaf elements: 0
## # lol_path():
## # A tibble: 0 × 3
## # … with 3 variables: path <chr>, n <int>, is_leaf <lgl>

lol_pull() extracts a path from the lol as a vector; lol_lpull() extracts paths as lists.

titles <- lol_pull(lol, "hits[*].projects[*].projectTitle")
length(titles)
## [1] 237
head(titles, 2)
## [1] "1.3 Million Brain Cells from E18 Mice"                                      
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"

3.2.3 Creating projects() tibbles with specific columns

The path or its abbreviation can be used to specify the columns of the tibble to be returned by the projects() query.

Here we retrieve additional details of donor count and total cells by adding appropriate path abbreviations to a named character vector. Names on the character vector can be used to rename the path more concisely, but the paths must uniquely identify elements in the list-of-lists.

columns <- c(
    projectId = "hits[*].entryId",
    projectTitle = "hits[*].projects[*].projectTitle",
    genusSpecies = "hits[*].donorOrganisms[*].genusSpecies[*]",
    donorCount = "hits[*].donorOrganisms[*].donorCount",
    cellSuspensions.organ = "hits[*].cellSuspensions[*].organ[*]",
    totalCells = "hits[*].cellSuspensions[*].totalCells"
)
projects <- projects(filters, columns = columns)
projects
## # A tibble: 17 × 6
##    projectId    projectTitle genusSpecies donorCount cellSuspensions… totalCells
##    <chr>        <chr>        <list>            <int> <list>           <list>    
##  1 c1810dbc-16… A cell atla… <chr [2]>            24 <chr [2]>        <int [2]> 
##  2 c0518445-3b… A cellular … <chr [1]>            17 <chr [2]>        <int [2]> 
##  3 73769e0a-5f… A proximal-… <chr [1]>             3 <chr [2]>        <int [0]> 
##  4 957261f7-2b… A spatial m… <chr [1]>            13 <chr [1]>        <int [0]> 
##  5 1dddae6e-37… Cell Types … <chr [1]>             6 <chr [1]>        <int [0]> 
##  6 ad98d3cd-26… Cells of th… <chr [1]>            14 <chr [1]>        <int [1]> 
##  7 fde199d2-a8… Cells of th… <chr [1]>            12 <chr [4]>        <int [0]> 
##  8 83f5188e-3b… Distinct mi… <chr [1]>             6 <chr [2]>        <int [2]> 
##  9 2f676143-80… Integrative… <chr [1]>            15 <chr [1]>        <int [0]> 
## 10 c4077b3c-5c… Ischaemic s… <chr [1]>            14 <chr [3]>        <int [3]> 
## 11 091cf39b-01… Profiling o… <chr [1]>             3 <chr [1]>        <int [1]> 
## 12 f83165c5-e2… Reconstruct… <chr [1]>            16 <chr [3]>        <int [0]> 
## 13 31887183-a7… Single-nucl… <chr [1]>            16 <chr [7]>        <int [0]> 
## 14 abe1a013-af… Spatio-temp… <chr [1]>             8 <chr [1]>        <int [0]> 
## 15 b963bd4b-4b… The cellula… <chr [1]>           120 <chr [1]>        <int [1]> 
## 16 4e6f083b-5b… The emergen… <chr [1]>             6 <chr [3]>        <int [3]> 
## 17 455b46e6-d8… Transcripto… <chr [1]>             4 <chr [3]>        <int [3]>

Note that the cellSuspensions.organ and totalCells columns have more than one entry per project.

projects |>
   select(projectId, cellSuspensions.organ, totalCells)
## # A tibble: 17 × 3
##    projectId                            cellSuspensions.organ totalCells
##    <chr>                                <list>                <list>    
##  1 c1810dbc-16d2-45c3-b45e-3e675f88d87b <chr [2]>             <int [2]> 
##  2 c0518445-3b3b-49c6-b8fc-c41daa4eacba <chr [2]>             <int [2]> 
##  3 73769e0a-5fcd-41f4-9083-41ae08bfa4c1 <chr [2]>             <int [0]> 
##  4 957261f7-2bd6-4358-a6ed-24ee080d5cfc <chr [1]>             <int [0]> 
##  5 1dddae6e-3753-48af-b20e-fa22abad125d <chr [1]>             <int [0]> 
##  6 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 <chr [1]>             <int [1]> 
##  7 fde199d2-a841-4ed1-aa65-b9e0af8969b1 <chr [4]>             <int [0]> 
##  8 83f5188e-3bf7-4956-9544-cea4f8997756 <chr [2]>             <int [2]> 
##  9 2f676143-80c2-4bc6-b7b4-2613fe0fadf0 <chr [1]>             <int [0]> 
## 10 c4077b3c-5c98-4d26-a614-246d12c2e5d7 <chr [3]>             <int [3]> 
## 11 091cf39b-01bc-42e5-9437-f419a66c8a45 <chr [1]>             <int [1]> 
## 12 f83165c5-e2ea-4d15-a5cf-33f3550bffde <chr [3]>             <int [0]> 
## 13 31887183-a72c-4308-9eac-c6140313f39c <chr [7]>             <int [0]> 
## 14 abe1a013-af7a-45ed-8c26-f3793c24a1f4 <chr [1]>             <int [0]> 
## 15 b963bd4b-4bc1-4404-8425-69d74bc636b8 <chr [1]>             <int [1]> 
## 16 4e6f083b-5b9a-4393-9890-2a83da8188f1 <chr [3]>             <int [3]> 
## 17 455b46e6-d8ea-4611-861e-de720a562ada <chr [3]>             <int [3]>

In this case, the mapping between cellSuspensions.organ and totalCells is clear, but in general more refined navigation of the lol structure may be necessary.

projects |>
    select(projectId, cellSuspensions.organ, totalCells) |>
    filter(lengths(totalCells) > 0) |>
    tidyr::unnest(c("cellSuspensions.organ", "totalCells"))
## # A tibble: 18 × 3
##    projectId                            cellSuspensions.organ totalCells
##    <chr>                                <chr>                      <int>
##  1 c1810dbc-16d2-45c3-b45e-3e675f88d87b thymus                    456000
##  2 c1810dbc-16d2-45c3-b45e-3e675f88d87b colon                      16000
##  3 c0518445-3b3b-49c6-b8fc-c41daa4eacba lung                       40200
##  4 c0518445-3b3b-49c6-b8fc-c41daa4eacba nose                        7087
##  5 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 heart                     791000
##  6 83f5188e-3bf7-4956-9544-cea4f8997756 immune organ                 381
##  7 83f5188e-3bf7-4956-9544-cea4f8997756 large intestine             1141
##  8 c4077b3c-5c98-4d26-a614-246d12c2e5d7 esophagus                  93267
##  9 c4077b3c-5c98-4d26-a614-246d12c2e5d7 spleen                     66553
## 10 c4077b3c-5c98-4d26-a614-246d12c2e5d7 lung                       40025
## 11 091cf39b-01bc-42e5-9437-f419a66c8a45 bone marrow              1480000
## 12 b963bd4b-4bc1-4404-8425-69d74bc636b8 blood                     800000
## 13 4e6f083b-5b9a-4393-9890-2a83da8188f1 embryo                     27083
## 14 4e6f083b-5b9a-4393-9890-2a83da8188f1 endoderm                   54166
## 15 4e6f083b-5b9a-4393-9890-2a83da8188f1 presumptive gut            30952
## 16 455b46e6-d8ea-4611-861e-de720a562ada bone marrow                87532
## 17 455b46e6-d8ea-4611-861e-de720a562ada spleen                     60043
## 18 455b46e6-d8ea-4611-861e-de720a562ada blood                      25016

Select the following entry, augment the filter, and query available files

projects %>%
    filter(startsWith(projectTitle, "Reconstruct")) %>%
    t()
##                       [,1]                                                                                                 
## projectId             "f83165c5-e2ea-4d15-a5cf-33f3550bffde"                                                               
## projectTitle          "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"
## genusSpecies          "Homo sapiens"                                                                                       
## donorCount            16                                                                                                   
## cellSuspensions.organ character,3                                                                                          
## totalCells            integer,0

This approach can be used to customize the tibbles returned by the other main functions in the package, files(), samples(), and bundles().

3.3 File download

The relevant file can be selected and downloaded using the technique in the first example.

filters <- filters(
    projectId = list(is = "f83165c5-e2ea-4d15-a5cf-33f3550bffde"),
    fileFormat = list(is = "h5ad")
)
files <-
    files(filters) %>%
    head(1)            # only first file, for demonstration
files %>% t()
##              [,1]                                                                                                                                                      
## fileId       "6d4fedcf-857d-5fbb-9928-8b9605500a69"                                                                                                                    
## name         "vento18_ss2.processed.h5ad"                                                                                                                              
## fileFormat   "h5ad"                                                                                                                                                    
## size         "82121633"                                                                                                                                                
## version      "2021-02-10T16:56:40.419579Z"                                                                                                                             
## projectTitle "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"                                                     
## projectId    "f83165c5-e2ea-4d15-a5cf-33f3550bffde"                                                                                                                    
## url          "https://service.azul.data.humancellatlas.org/repository/files/6d4fedcf-857d-5fbb-9928-8b9605500a69?catalog=dcp15&version=2021-02-10T16%3A56%3A40.419579Z"
file_path <- files_download(files)

"h5ad" files can be read as SingleCellExperiment objects using the zellkonverter package.

## don't want large amount of data read from disk
sce <- zellkonverter::readH5AD(file_path, use_hdf5 = TRUE)
sce

4 Example: A multiple file download

project_filter <- filters(fileFormat = list(is = "csv"))
project_tibble <- projects(project_filter)

project_tibble %>%
    filter(
        startsWith(
            projectTitle,
            "Reconstructing the human first trimester"
        )
    )
## # A tibble: 1 × 5
##   projectId              projectTitle genusSpecies samples.organ specimens.organ
##   <chr>                  <chr>        <list>       <list>        <list>         
## 1 f83165c5-e2ea-4d15-a5… Reconstruct… <chr [1]>    <chr [3]>     <chr [3]>

projectId <-
    project_tibble %>%
    filter(
        startsWith(
            projectTitle,
            "Reconstructing the human first trimester"
        )
    ) %>%
    pull(projectId)

file_filter <- filters(
    projectId = list(is = projectId),
    fileFormat = list(is = "csv")
)

## first 4 files will be returned
file_tibble <- files(file_filter, size = 4)

file_tibble %>%
    files_download()
## 7f9a181e-24c5-5462-b308-7fef5b1bda2a-2021-02-10T16:56:40.419579Z 
## "/home/biocbuild/.cache/R/hca/372fcc60a648de_372fcc60a648de.csv" 
## d04c6e3c-b740-5586-8420-4480a1b5706c-2021-02-10T16:56:40.419579Z 
## "/home/biocbuild/.cache/R/hca/372fcc22f276fe_372fcc22f276fe.csv" 
## d30ffc0b-7d6e-5b85-aff9-21ec69663a81-2021-02-10T16:56:40.419579Z 
## "/home/biocbuild/.cache/R/hca/372fcc2643c2b7_372fcc2643c2b7.csv" 
## e1517725-01b0-5346-9788-afca63e9993a-2021-02-10T16:56:40.419579Z 
##     "/home/biocbuild/.cache/R/hca/372fcc758ae5_372fcc758ae5.csv"

5 Example: Exploring the pagination feature

The files(), bundles(), and samples() can all return many 1000’s of results. It is necessary to ‘page’ through these to see all of them. We illustrate pagination with projects(), retrieving only 30 projects.

Pagination works for the default tibble output

page_1_tbl <- projects(size = 30)
page_1_tbl
## # A tibble: 30 × 5
##    projectId             projectTitle genusSpecies samples.organ specimens.organ
##    <chr>                 <chr>        <list>       <list>        <list>         
##  1 74b6d569-3b11-42ef-b… 1.3 Million… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 53c53cd4-8127-4e12-b… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  4 60ea42e1-af49-42f5-8… A Protocol … <chr [1]>    <chr [1]>     <chr [1]>      
##  5 ef1e3497-515e-4bbe-8… A Single-Ce… <chr [1]>    <chr [3]>     <chr [3]>      
##  6 f86f1ab4-1fbb-4510-a… A Single-Ce… <chr [2]>    <chr [1]>     <chr [1]>      
##  7 602628d7-c038-48a8-a… A Single-ce… <chr [1]>    <chr [3]>     <chr [3]>      
##  8 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]>    <chr [2]>     <chr [2]>      
##  9 c0518445-3b3b-49c6-b… A cellular … <chr [1]>    <chr [2]>     <chr [2]>      
## 10 5116c081-8be7-49c5-8… A comprehen… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 20 more rows

page_2_tbl <- page_1_tbl %>% hca_next()
page_2_tbl
## # A tibble: 30 × 5
##    projectId             projectTitle genusSpecies samples.organ specimens.organ
##    <chr>                 <chr>        <chr>        <list>        <list>         
##  1 0fd8f918-62d6-4b8b-a… An Atlas of… Homo sapiens <chr [1]>     <chr [1]>      
##  2 8ab8726d-81b9-4bd2-a… An organoid… Homo sapiens <chr [5]>     <chr [5]>      
##  3 005d611a-14d5-4fbf-8… Assessing t… Homo sapiens <chr [0]>     <chr [1]>      
##  4 04ad400c-58cb-40a5-b… Blood and i… Homo sapiens <chr [4]>     <chr [4]>      
##  5 a29952d9-925e-40f4-8… Bone marrow… Homo sapiens <chr [1]>     <chr [1]>      
##  6 74493e98-44fc-48b0-a… CD27hiCD38h… Homo sapiens <chr [1]>     <chr [1]>      
##  7 7ac8822c-4ef0-4194-a… COVID-19 se… Homo sapiens <chr [1]>     <chr [1]>      
##  8 da2747fa-2921-42e0-a… Capturing h… Homo sapiens <chr [0]>     <chr [1]>      
##  9 1dddae6e-3753-48af-b… Cell Types … Homo sapiens <chr [1]>     <chr [2]>      
## 10 f81efc03-9f56-4354-a… Cell hashin… Homo sapiens <chr [1]>     <chr [1]>      
## # … with 20 more rows

## should be identical to page_1_tbl
page_2_tbl %>% hca_prev()
## # A tibble: 30 × 5
##    projectId             projectTitle genusSpecies samples.organ specimens.organ
##    <chr>                 <chr>        <list>       <list>        <list>         
##  1 74b6d569-3b11-42ef-b… 1.3 Million… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 53c53cd4-8127-4e12-b… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]>    <chr [1]>     <chr [1]>      
##  4 60ea42e1-af49-42f5-8… A Protocol … <chr [1]>    <chr [1]>     <chr [1]>      
##  5 ef1e3497-515e-4bbe-8… A Single-Ce… <chr [1]>    <chr [3]>     <chr [3]>      
##  6 f86f1ab4-1fbb-4510-a… A Single-Ce… <chr [2]>    <chr [1]>     <chr [1]>      
##  7 602628d7-c038-48a8-a… A Single-ce… <chr [1]>    <chr [3]>     <chr [3]>      
##  8 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]>    <chr [2]>     <chr [2]>      
##  9 c0518445-3b3b-49c6-b… A cellular … <chr [1]>    <chr [2]>     <chr [2]>      
## 10 5116c081-8be7-49c5-8… A comprehen… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 20 more rows

Pagination also works for the lol objects

page_1_lol <- projects(size = 5, as = "lol")
page_1_lol %>%
    lol_pull("hits[*].projects[*].projectTitle")
## [1] "1.3 Million Brain Cells from E18 Mice"                                                                 
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"                           
## [3] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."                                              
## [4] "A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva"
## [5] "A Single-Cell Atlas of the Human Healthy Airways."

page_2_lol <-
    page_1_lol %>%
    hca_next()
page_2_lol %>%
    lol_pull("hits[*].projects[*].projectTitle")
## [1] "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"
## [2] "A Single-cell Transcriptomic Atlas of Human Intervertebral Disc"                                                    
## [3] "A cell atlas of human thymic development defines T cell repertoire formation"                                       
## [4] "A cellular census of human lungs identifies novel cell states in health and in asthma"                              
## [5] "A comprehensive single cell transcriptional landscape of human hematopoietic progenitors"

## should be identical to page_1_lol
page_2_lol %>%
    hca_prev() %>%
    lol_pull("hits[*].projects[*].projectTitle")
## [1] "1.3 Million Brain Cells from E18 Mice"                                                                 
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"                           
## [3] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."                                              
## [4] "A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva"
## [5] "A Single-Cell Atlas of the Human Healthy Airways."

6 Example: Obtaining other data entities

Much like projects() and files(), samples() and bundles() allow you to provide a filter object and additional criteria to retrieve data in the form of samples and bundles respectively

heart_filters <- filters(organ = list(is = "heart"))
heart_samples <- samples(filters = heart_filters, size = 4)
heart_samples
## # A tibble: 4 × 6
##   entryId                         projectTitle genusSpecies disease format count
##   <chr>                           <chr>        <chr>        <chr>   <list> <lis>
## 1 012c52ff-4770-4c0c-8c2e-c348da… A Cellular … Mus musculus normal  <chr>  <int>
## 2 035db5b9-a219-4df8-bfc9-117cd0… A Cellular … Mus musculus normal  <chr>  <int>
## 3 09e425f7-22d7-487e-b78b-78b449… A Cellular … Mus musculus normal  <chr>  <int>
## 4 2273e44d-9fbc-4c13-8cb3-3caf8a… A Cellular … Mus musculus normal  <chr>  <int>

heart_bundles <- bundles(filters = heart_filters, size = 4)
heart_bundles
## # A tibble: 4 × 6
##   projectTitle               genusSpecies samples files bundleUuid bundleVersion
##   <chr>                      <chr>        <list>  <lis> <chr>      <chr>        
## 1 A Cellular Atlas of Pitx2… Mus musculus <chr>   <chr> 0d391bd1-… 2021-02-26T0…
## 2 A Cellular Atlas of Pitx2… Mus musculus <chr>   <chr> 165a2df1-… 2021-02-26T0…
## 3 A Cellular Atlas of Pitx2… Mus musculus <chr>   <chr> 166c1b1a-… 2020-08-04T1…
## 4 A Cellular Atlas of Pitx2… Mus musculus <chr>   <chr> 18bad6b1-… 2021-02-26T0…

7 Example: Obtaining summaries of project catalogs

HCA experiments are organized into catalogs, each of which can be summarized with the summary() function

heart_filters <- filters(organ = list(is = "heart"))
summary(filters = heart_filters, type = "fileTypeSummaries")
## # A tibble: 11 × 3
##    format   count     totalSize
##    <chr>    <int>         <dbl>
##  1 fastq.gz 28284 6670325013979
##  2 loom       169  355865926256
##  3 bam        164 3284598129743
##  4 tsv.gz      49      49919933
##  5 mtx.gz      24     479611217
##  6 bed.gz       6    3332206567
##  7 .txt         4      80206910
##  8 RDS          3     301293176
##  9 Rds          3    2637887113
## 10 h5ad         2    2027243221
## 11 h5ad.zip     1   15510167649
first_catalog <- catalogs()[1]
summary(type = "overview", catalog = first_catalog)
## # A tibble: 7 × 2
##   name            value
##   <chr>           <dbl>
## 1 projectCount  2.37e 2
## 2 specimenCount 1.14e 4
## 3 speciesCount  2   e 0
## 4 fileCount     4.66e 5
## 5 totalFileSize 1.58e14
## 6 donorCount    3.32e 3
## 7 labCount      4.06e 2

8 Example: Obtaining details on individual projects, files, samples, and bundles

Each project, file, sample, and bundles has its own unique ID by which, in conjunction with its catalog, can be to uniquely identify them.

heart_filters <- filters(organ = list(is = "heart"))
heart_projects <- projects(filters = heart_filters, size = 4)
heart_projects
## # A tibble: 4 × 5
##   projectId              projectTitle genusSpecies samples.organ specimens.organ
##   <chr>                  <chr>        <chr>        <list>        <list>         
## 1 7027adc6-c9c9-46f3-84… A Cellular … Mus musculus <chr [1]>     <chr [1]>      
## 2 a9301beb-e9fa-42fe-b7… A human cel… Homo sapiens <chr [14]>    <chr [14]>     
## 3 c31fa434-c9ed-4263-a9… A single-ce… Homo sapiens <chr [18]>    <chr [18]>     
## 4 ad98d3cd-26fb-4ee3-99… Cells of th… Homo sapiens <chr [1]>     <chr [1]>

projectId <-
    heart_projects %>%
    filter(
        startsWith(
            projectTitle,
            "Cells of the adult human"
        )
    ) %>%
    dplyr::pull(projectId)

projects_detail(uuid = projectId)
## $protocols
## $protocols[[1]]
## $protocols[[1]]$workflow
## $protocols[[1]]$workflow[[1]]
## [1] "optimus_post_processing_v1.0.0"
## 
## $protocols[[1]]$workflow[[2]]
## [1] "optimus_v4.2.2"
## 
## 
## 
## $protocols[[2]]
## $protocols[[2]]$libraryConstructionApproach
## $protocols[[2]]$libraryConstructionApproach[[1]]
## [1] "10X 3' v2 sequencing"
## 
## $protocols[[2]]$libraryConstructionApproach[[2]]
## [1] "10x 3' v3 sequencing"
## 
## 
## $protocols[[2]]$nucleicAcidSource
## $protocols[[2]]$nucleicAcidSource[[1]]
## [1] "single cell"
## 
## $protocols[[2]]$nucleicAcidSource[[2]]
## [1] "single nucleus"
## 
## 
## 
## $protocols[[3]]
## $protocols[[3]]$instrumentManufacturerModel
## $protocols[[3]]$instrumentManufacturerModel[[1]]
## [1] "Illumina HiSeq 4000"
## 
## $protocols[[3]]$instrumentManufacturerModel[[2]]
## [1] "Illumina NextSeq 500"
## 
## 
## $protocols[[3]]$pairedEnd
## $protocols[[3]]$pairedEnd[[1]]
## [1] FALSE
## 
## 
## 
## 
## $entryId
## [1] "ad98d3cd-26fb-4ee3-99c9-8a2ab085e737"
## 
## $sources
## $sources[[1]]
## $sources[[1]]$sourceId
## [1] "5da1ec4d-a462-4bf0-9ee1-4b76d8199241"
## 
## $sources[[1]]$sourceSpec
## [1] "tdr:datarepo-4a3b719a:snapshot/hca_prod_ad98d3cd26fb4ee399c98a2ab085e737__20220118_dcp2_20220121_dcp12:/0"
## 
## 
## 
## $projects
## $projects[[1]]
## $projects[[1]]$projectId
## [1] "ad98d3cd-26fb-4ee3-99c9-8a2ab085e737"
## 
## $projects[[1]]$projectTitle
## [1] "Cells of the adult human heart"
## 
## $projects[[1]]$projectShortname
## [1] "HeartSingleCellsAndNucleiSeq"
## 
## $projects[[1]]$laboratory
## $projects[[1]]$laboratory[[1]]
## [1] "Cardiovascular Division"
## 
## $projects[[1]]$laboratory[[2]]
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$laboratory[[3]]
## [1] "Cellular Genetics"
## 
## $projects[[1]]$laboratory[[4]]
## [1] "Department of Genetics"
## 
## $projects[[1]]$laboratory[[5]]
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
## 
## $projects[[1]]$laboratory[[6]]
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$laboratory[[7]]
## [1] "Human Cell Atlas Data Coordination Platform"
## 
## $projects[[1]]$laboratory[[8]]
## [1] "Institute of Computational Biology (ICB)"
## 
## $projects[[1]]$laboratory[[9]]
## [1] "National Heart and Lung Institute"
## 
## 
## $projects[[1]]$estimatedCellCount
## NULL
## 
## $projects[[1]]$projectDescription
## [1] "Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require deeper understanding of the healthy heart’s molecular processes. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using state-of-the-art analyses of large-scale single-cell and nuclei transcriptomes, we characterise six anatomical adult heart regions (left/right atria and ventricles, apex, interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct atrial and ventricular subsets with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment we identify cardiac resident macrophages with inflammatory and protective transcriptional signatures. Further, inference of cell-cell interactions highlight different macrophage-fibroblast-cardiomyocyte networks between atria and ventricles that are distinct from skeletal muscle.  We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease."
## 
## $projects[[1]]$contributors
## $projects[[1]]$contributors[[1]]
## $projects[[1]]$contributors[[1]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[1]]$contactName
## [1] "Michela,,Noseda"
## 
## $projects[[1]]$contributors[[1]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[1]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[1]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[1]]$email
## [1] "m.noseda@imperial.ac.uk"
## 
## 
## $projects[[1]]$contributors[[2]]
## $projects[[1]]$contributors[[2]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[2]]$contactName
## [1] "Monika,,Litviňuková"
## 
## $projects[[1]]$contributors[[2]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[2]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[2]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[2]]$email
## [1] "monika.litvinukova@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[3]]
## $projects[[1]]$contributors[[3]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[3]]$contactName
## [1] "Daniel,,Reichart"
## 
## $projects[[1]]$contributors[[3]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[3]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[3]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[3]]$email
## [1] "Daniel_Reichart@hms.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[4]]
## $projects[[1]]$contributors[[4]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[4]]$contactName
## [1] "Masatoshi,,Kanda"
## 
## $projects[[1]]$contributors[[4]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[4]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[4]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[4]]$email
## [1] "masatoshi.kanda@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[5]]
## $projects[[1]]$contributors[[5]]$institution
## [1] "Brigham and Women’s Hospital"
## 
## $projects[[1]]$contributors[[5]]$contactName
## [1] "Barbara,,McDonough"
## 
## $projects[[1]]$contributors[[5]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[5]]$laboratory
## [1] "Cardiovascular Division"
## 
## $projects[[1]]$contributors[[5]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[5]]$email
## [1] "mcdonough@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[6]]
## $projects[[1]]$contributors[[6]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[6]]$contactName
## [1] "Emily,,Nadelmann"
## 
## $projects[[1]]$contributors[[6]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[6]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[6]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[6]]$email
## [1] "Emily_Nadelmann@hms.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[7]]
## $projects[[1]]$contributors[[7]]$institution
## [1] "University of Alberta"
## 
## $projects[[1]]$contributors[[7]]$contactName
## [1] "Anissa,,Viveiros"
## 
## $projects[[1]]$contributors[[7]]$projectRole
## [1] "biomaterial provider"
## 
## $projects[[1]]$contributors[[7]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$contributors[[7]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[7]]$email
## [1] "aviveiro@ualberta.ca"
## 
## 
## $projects[[1]]$contributors[[8]]
## $projects[[1]]$contributors[[8]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[8]]$contactName
## [1] "Joshua,M,Gorham"
## 
## $projects[[1]]$contributors[[8]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[8]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[8]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[8]]$email
## [1] "jgorham@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[9]]
## $projects[[1]]$contributors[[9]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
## 
## $projects[[1]]$contributors[[9]]$contactName
## [1] "Krishnaa,T.,Mahbubani"
## 
## $projects[[1]]$contributors[[9]]$projectRole
## [1] "biomaterial provider"
## 
## $projects[[1]]$contributors[[9]]$laboratory
## NULL
## 
## $projects[[1]]$contributors[[9]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[9]]$email
## [1] "ktam2@cam.ac.uk"
## 
## 
## $projects[[1]]$contributors[[10]]
## $projects[[1]]$contributors[[10]]$institution
## [1] "HMGU"
## 
## $projects[[1]]$contributors[[10]]$contactName
## [1] "Matthias,,Heinig"
## 
## $projects[[1]]$contributors[[10]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[10]]$laboratory
## [1] "Institute of Computational Biology (ICB)"
## 
## $projects[[1]]$contributors[[10]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[10]]$email
## [1] "matthias.heinig@helmholtz-muenchen.de"
## 
## 
## $projects[[1]]$contributors[[11]]
## $projects[[1]]$contributors[[11]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[11]]$contactName
## [1] "J.,G.,Seidman"
## 
## $projects[[1]]$contributors[[11]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[11]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[11]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[11]]$email
## [1] "seidman@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[12]]
## $projects[[1]]$contributors[[12]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[12]]$contactName
## [1] "Christine,,Seidman"
## 
## $projects[[1]]$contributors[[12]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[12]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[12]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[12]]$email
## [1] "cseidman@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[13]]
## $projects[[1]]$contributors[[13]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
## 
## $projects[[1]]$contributors[[13]]$contactName
## [1] "Kourosh,,Saeb-Parsy"
## 
## $projects[[1]]$contributors[[13]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[13]]$laboratory
## NULL
## 
## $projects[[1]]$contributors[[13]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[13]]$email
## [1] "ks10014@cam.ac.uk"
## 
## 
## $projects[[1]]$contributors[[14]]
## $projects[[1]]$contributors[[14]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[14]]$contactName
## [1] "Giannino,,Patone"
## 
## $projects[[1]]$contributors[[14]]$projectRole
## [1] "computational scientist"
## 
## $projects[[1]]$contributors[[14]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[14]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[14]]$email
## [1] "Giannino.Patone@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[15]]
## $projects[[1]]$contributors[[15]]$institution
## [1] "Sun-Yat Sen University"
## 
## $projects[[1]]$contributors[[15]]$contactName
## [1] "Hongbo,,Zhang"
## 
## $projects[[1]]$contributors[[15]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[15]]$laboratory
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
## 
## $projects[[1]]$contributors[[15]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[15]]$email
## [1] "hz3@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[16]]
## $projects[[1]]$contributors[[16]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[16]]$contactName
## [1] "Eric,L.,Lindberg"
## 
## $projects[[1]]$contributors[[16]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[16]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[16]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[16]]$email
## [1] "Eric.Lindberg@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[17]]
## $projects[[1]]$contributors[[17]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[17]]$contactName
## [1] "Henrike,,Maatz"
## 
## $projects[[1]]$contributors[[17]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[17]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[17]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[17]]$email
## [1] "h.maatz@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[18]]
## $projects[[1]]$contributors[[18]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[18]]$contactName
## [1] "Joseph,J.,Boyle"
## 
## $projects[[1]]$contributors[[18]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[18]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[18]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[18]]$email
## [1] "joseph.boyle@imperial.ac.uk"
## 
## 
## $projects[[1]]$contributors[[19]]
## $projects[[1]]$contributors[[19]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[19]]$contactName
## [1] "Liz,,Tuck"
## 
## $projects[[1]]$contributors[[19]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[19]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[19]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[19]]$email
## [1] "et2@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[20]]
## $projects[[1]]$contributors[[20]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[20]]$contactName
## [1] "Sarah,A.,Teichmann"
## 
## $projects[[1]]$contributors[[20]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[20]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[20]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[20]]$email
## [1] "st9@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[21]]
## $projects[[1]]$contributors[[21]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[21]]$contactName
## [1] "Omer,,Bayraktar"
## 
## $projects[[1]]$contributors[[21]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[21]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[21]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[21]]$email
## [1] "ob5@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[22]]
## $projects[[1]]$contributors[[22]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[22]]$contactName
## [1] "Eirini,S.,Fasouli"
## 
## $projects[[1]]$contributors[[22]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[22]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[22]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[22]]$email
## [1] "ef5@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[23]]
## $projects[[1]]$contributors[[23]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[23]]$contactName
## [1] "Kenny,,Roberts"
## 
## $projects[[1]]$contributors[[23]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[23]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[23]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[23]]$email
## [1] "kr19@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[24]]
## $projects[[1]]$contributors[[24]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[24]]$contactName
## [1] "Daniel,,DeLaughter"
## 
## $projects[[1]]$contributors[[24]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[24]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[24]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[24]]$email
## [1] "Daniel_DeLaughter@hms.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[25]]
## $projects[[1]]$contributors[[25]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[25]]$contactName
## [1] "Norbert,,Hübner"
## 
## $projects[[1]]$contributors[[25]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[25]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[25]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[25]]$email
## [1] "nhuebner@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[26]]
## $projects[[1]]$contributors[[26]]$institution
## [1] "EMBL-EBI"
## 
## $projects[[1]]$contributors[[26]]$contactName
## [1] "Marion,F,Shadbolt"
## 
## $projects[[1]]$contributors[[26]]$projectRole
## [1] "data curator"
## 
## $projects[[1]]$contributors[[26]]$laboratory
## [1] "Human Cell Atlas Data Coordination Platform"
## 
## $projects[[1]]$contributors[[26]]$correspondingContributor
## [1] FALSE
## 
## $projects[[1]]$contributors[[26]]$email
## [1] "mshadbolt@ebi.ac.uk"
## 
## 
## $projects[[1]]$contributors[[27]]
## $projects[[1]]$contributors[[27]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[27]]$contactName
## [1] "Carlos,,Talavera-López"
## 
## $projects[[1]]$contributors[[27]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[27]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[27]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[27]]$email
## [1] "ct5@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[28]]
## $projects[[1]]$contributors[[28]]$institution
## [1] "University of Alberta"
## 
## $projects[[1]]$contributors[[28]]$contactName
## [1] "Hao,,Zhang"
## 
## $projects[[1]]$contributors[[28]]$projectRole
## [1] "biomaterial provider"
## 
## $projects[[1]]$contributors[[28]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$contributors[[28]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[28]]$email
## [1] "hzhang10@ualberta.ca"
## 
## 
## $projects[[1]]$contributors[[29]]
## $projects[[1]]$contributors[[29]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[29]]$contactName
## [1] "Krzysztof,,Polanski"
## 
## $projects[[1]]$contributors[[29]]$projectRole
## [1] "computational scientist"
## 
## $projects[[1]]$contributors[[29]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[29]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[29]]$email
## [1] "kp9@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[30]]
## $projects[[1]]$contributors[[30]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[30]]$contactName
## [1] "Hiroko,,Wakimoto"
## 
## $projects[[1]]$contributors[[30]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[30]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[30]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[30]]$email
## [1] "hwakimoto@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[31]]
## $projects[[1]]$contributors[[31]]$institution
## [1] "University of Alberta"
## 
## $projects[[1]]$contributors[[31]]$contactName
## [1] "Gavin,,Oudit"
## 
## $projects[[1]]$contributors[[31]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[31]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$contributors[[31]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[31]]$email
## [1] "gavin.oudit@ualberta.ca"
## 
## 
## $projects[[1]]$contributors[[32]]
## $projects[[1]]$contributors[[32]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[32]]$contactName
## [1] "Catherine,L.,Worth"
## 
## $projects[[1]]$contributors[[32]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[32]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[32]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[32]]$email
## [1] "catherine.sargent@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[33]]
## $projects[[1]]$contributors[[33]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[33]]$contactName
## [1] "Michael,,Lee"
## 
## $projects[[1]]$contributors[[33]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[33]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[33]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[33]]$email
## [1] "michael.lee@imperial.ac.uk"
## 
## 
## $projects[[1]]$contributors[[34]]
## $projects[[1]]$contributors[[34]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[34]]$contactName
## [1] "Sara,,Samari"
## 
## $projects[[1]]$contributors[[34]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[34]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[34]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[34]]$email
## [1] "sara.samari13@imperial.ac.uk"
## 
## 
## 
## $projects[[1]]$publications
## $projects[[1]]$publications[[1]]
## $projects[[1]]$publications[[1]]$publicationTitle
## [1] "Cells of the adult human heart"
## 
## $projects[[1]]$publications[[1]]$officialHcaPublication
## NULL
## 
## $projects[[1]]$publications[[1]]$publicationUrl
## [1] "https://www.nature.com/articles/s41586-020-2797-4"
## 
## $projects[[1]]$publications[[1]]$doi
## [1] "10.1038/s41586-020-2797-4"
## 
## 
## 
## $projects[[1]]$supplementaryLinks
## $projects[[1]]$supplementaryLinks[[1]]
## [1] "https://www.heartcellatlas.org/"
## 
## 
## $projects[[1]]$matrices
## $projects[[1]]$matrices$genusSpecies
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$format
## [1] "loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$name
## [1] "human-heart-10XV3.loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$sha256
## [1] "ee31af654eb2008c8748875b117ee7eecd70ad63ed93811144fb44651144c3ca"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$size
## [1] 3255905369
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b0cd671e-a918-51db-ba29-e127caf325c5"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-13T01:32:57.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b0cd671e-a918-51db-ba29-e127caf325c5?catalog=dcp15&version=2021-02-13T01%3A32%3A57.000000Z"
## 
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "human-heart-10XV2.loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "d38c4fe7ef2bfb28f42854e447ba65929bbcd89023211c1bff0e34674bede78e"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 4398007571
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?catalog=dcp15&version=2021-02-15T14%3A15%3A05.000000Z"
## 
## 
## 
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "human-heart-10XV2.loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "d38c4fe7ef2bfb28f42854e447ba65929bbcd89023211c1bff0e34674bede78e"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 4398007571
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?catalog=dcp15&version=2021-02-15T14%3A15%3A05.000000Z"
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## $projects[[1]]$contributedAnalyses
## $projects[[1]]$contributedAnalyses$genusSpecies
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Matrix"
## 
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "h5ad"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "hca_heart_global_ctl200723_freeze.h5ad"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "80917c4e67e581ee2696691ddd4b031bf45cbc7ba77757c8a203cd88c15f9c3f"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 5068859764
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "Contributor"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "b30d1a16-fb04-5ac7-999f-6ce9d1de0c76"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-10T17:01:03.177554Z"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?catalog=dcp15&version=2021-02-10T17%3A01%3A03.177554Z"
## 
## 
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription[[1]]
## [1] "Matrix"
## 
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$format
## [1] "h5ad"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$name
## [1] "hca_heart_global_ctl200723_freeze.h5ad"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$sha256
## [1] "80917c4e67e581ee2696691ddd4b031bf45cbc7ba77757c8a203cd88c15f9c3f"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$size
## [1] 5068859764
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$fileSource
## [1] "Contributor"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b30d1a16-fb04-5ac7-999f-6ce9d1de0c76"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-10T17:01:03.177554Z"
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?catalog=dcp15&version=2021-02-10T17%3A01%3A03.177554Z"
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## $projects[[1]]$accessions
## $projects[[1]]$accessions[[1]]
## $projects[[1]]$accessions[[1]]$namespace
## [1] "biostudies"
## 
## $projects[[1]]$accessions[[1]]$accession
## [1] "S-SUBS13"
## 
## 
## $projects[[1]]$accessions[[2]]
## $projects[[1]]$accessions[[2]]$namespace
## [1] "insdc_project"
## 
## $projects[[1]]$accessions[[2]]$accession
## [1] "ERP123138"
## 
## 
## $projects[[1]]$accessions[[3]]
## $projects[[1]]$accessions[[3]]$namespace
## [1] "insdc_study"
## 
## $projects[[1]]$accessions[[3]]$accession
## [1] "PRJEB39602"
## 
## 
## 
## $projects[[1]]$accessible
## [1] TRUE
## 
## 
## 
## $samples
## $samples[[1]]
## $samples[[1]]$sampleEntityType
## $samples[[1]]$sampleEntityType[[1]]
## [1] "specimens"
## 
## 
## $samples[[1]]$effectiveOrgan
## $samples[[1]]$effectiveOrgan[[1]]
## [1] "heart"
## 
## 
## $samples[[1]]$id
## $samples[[1]]$id[[1]]
## [1] "CBTM-361B_AX"
## 
## $samples[[1]]$id[[2]]
## [1] "CBTM-361B_LA"
## 
## $samples[[1]]$id[[3]]
## [1] "CBTM-361B_LV"
## 
## $samples[[1]]$id[[4]]
## [1] "CBTM-361B_RV"
## 
## $samples[[1]]$id[[5]]
## [1] "CBTM-362C_AX"
## 
## $samples[[1]]$id[[6]]
## [1] "CBTM-362C_LA"
## 
## $samples[[1]]$id[[7]]
## [1] "CBTM-362C_LV"
## 
## $samples[[1]]$id[[8]]
## [1] "CBTM-362C_RA"
## 
## $samples[[1]]$id[[9]]
## [1] "CBTM-362C_RV"
## 
## $samples[[1]]$id[[10]]
## [1] "CBTM-362C_SP"
## 
## $samples[[1]]$id[[11]]
## [1] "CBTM-364B_AX"
## 
## $samples[[1]]$id[[12]]
## [1] "CBTM-364B_LA"
## 
## $samples[[1]]$id[[13]]
## [1] "CBTM-364B_LV"
## 
## $samples[[1]]$id[[14]]
## [1] "CBTM-364B_RA"
## 
## $samples[[1]]$id[[15]]
## [1] "CBTM-364B_RV"
## 
## $samples[[1]]$id[[16]]
## [1] "CBTM-364B_SP"
## 
## $samples[[1]]$id[[17]]
## [1] "CBTM-386C_AX"
## 
## $samples[[1]]$id[[18]]
## [1] "CBTM-386C_LA"
## 
## $samples[[1]]$id[[19]]
## [1] "CBTM-386C_LV"
## 
## $samples[[1]]$id[[20]]
## [1] "CBTM-386C_RA"
## 
## $samples[[1]]$id[[21]]
## [1] "CBTM-386C_RV"
## 
## $samples[[1]]$id[[22]]
## [1] "CBTM-386C_SP"
## 
## $samples[[1]]$id[[23]]
## [1] "CBTM-390C_AX"
## 
## $samples[[1]]$id[[24]]
## [1] "CBTM-390C_LA"
## 
## $samples[[1]]$id[[25]]
## [1] "CBTM-390C_LV"
## 
## $samples[[1]]$id[[26]]
## [1] "CBTM-390C_RA"
## 
## $samples[[1]]$id[[27]]
## [1] "CBTM-390C_RV"
## 
## $samples[[1]]$id[[28]]
## [1] "CBTM-390C_SP"
## 
## $samples[[1]]$id[[29]]
## [1] "CBTM-417C_AX"
## 
## $samples[[1]]$id[[30]]
## [1] "CBTM-417C_LA"
## 
## $samples[[1]]$id[[31]]
## [1] "CBTM-417C_LV"
## 
## $samples[[1]]$id[[32]]
## [1] "CBTM-417C_RA"
## 
## $samples[[1]]$id[[33]]
## [1] "CBTM-417C_RV"
## 
## $samples[[1]]$id[[34]]
## [1] "CBTM-417C_SP"
## 
## $samples[[1]]$id[[35]]
## [1] "CBTM-423C_AX"
## 
## $samples[[1]]$id[[36]]
## [1] "CBTM-423C_LA"
## 
## $samples[[1]]$id[[37]]
## [1] "CBTM-423C_LV"
## 
## $samples[[1]]$id[[38]]
## [1] "CBTM-423C_RA"
## 
## $samples[[1]]$id[[39]]
## [1] "CBTM-423C_RV"
## 
## $samples[[1]]$id[[40]]
## [1] "CBTM-423C_SP"
## 
## $samples[[1]]$id[[41]]
## [1] "CBTM-473C_AX"
## 
## $samples[[1]]$id[[42]]
## [1] "CBTM-473C_LA"
## 
## $samples[[1]]$id[[43]]
## [1] "CBTM-473C_LV"
## 
## $samples[[1]]$id[[44]]
## [1] "CBTM-473C_RA"
## 
## $samples[[1]]$id[[45]]
## [1] "CBTM-473C_RV"
## 
## $samples[[1]]$id[[46]]
## [1] "CBTM-473C_SP"
## 
## $samples[[1]]$id[[47]]
## [1] "H0015_AX"
## 
## $samples[[1]]$id[[48]]
## [1] "H0015_LA"
## 
## $samples[[1]]$id[[49]]
## [1] "H0015_LV"
## 
## $samples[[1]]$id[[50]]
## [1] "H0015_RA"
## 
## $samples[[1]]$id[[51]]
## [1] "H0015_RV"
## 
## $samples[[1]]$id[[52]]
## [1] "H0015_SP"
## 
## $samples[[1]]$id[[53]]
## [1] "H0020_AX"
## 
## $samples[[1]]$id[[54]]
## [1] "H0020_LA"
## 
## $samples[[1]]$id[[55]]
## [1] "H0020_LV"
## 
## $samples[[1]]$id[[56]]
## [1] "H0020_RA"
## 
## $samples[[1]]$id[[57]]
## [1] "H0020_RV"
## 
## $samples[[1]]$id[[58]]
## [1] "H0020_SP"
## 
## $samples[[1]]$id[[59]]
## [1] "H0025_AX"
## 
## $samples[[1]]$id[[60]]
## [1] "H0025_LA"
## 
## $samples[[1]]$id[[61]]
## [1] "H0025_LV"
## 
## $samples[[1]]$id[[62]]
## [1] "H0025_RA"
## 
## $samples[[1]]$id[[63]]
## [1] "H0025_RV"
## 
## $samples[[1]]$id[[64]]
## [1] "H0025_SP"
## 
## $samples[[1]]$id[[65]]
## [1] "H0026_AX"
## 
## $samples[[1]]$id[[66]]
## [1] "H0026_LA"
## 
## $samples[[1]]$id[[67]]
## [1] "H0026_LV"
## 
## $samples[[1]]$id[[68]]
## [1] "H0026_RA"
## 
## $samples[[1]]$id[[69]]
## [1] "H0026_RV"
## 
## $samples[[1]]$id[[70]]
## [1] "H0026_SP"
## 
## $samples[[1]]$id[[71]]
## [1] "H0035_AX"
## 
## $samples[[1]]$id[[72]]
## [1] "H0035_LA"
## 
## $samples[[1]]$id[[73]]
## [1] "H0035_LV"
## 
## $samples[[1]]$id[[74]]
## [1] "H0035_RA"
## 
## $samples[[1]]$id[[75]]
## [1] "H0035_RV"
## 
## $samples[[1]]$id[[76]]
## [1] "H0035_SP"
## 
## $samples[[1]]$id[[77]]
## [1] "H0037_AX"
## 
## $samples[[1]]$id[[78]]
## [1] "H0037_LA"
## 
## $samples[[1]]$id[[79]]
## [1] "H0037_LV"
## 
## $samples[[1]]$id[[80]]
## [1] "H0037_RA"
## 
## $samples[[1]]$id[[81]]
## [1] "H0037_RV"
## 
## $samples[[1]]$id[[82]]
## [1] "H0037_SP"
## 
## 
## $samples[[1]]$organ
## $samples[[1]]$organ[[1]]
## [1] "heart"
## 
## 
## $samples[[1]]$organPart
## $samples[[1]]$organPart[[1]]
## [1] "apex of heart"
## 
## $samples[[1]]$organPart[[2]]
## [1] "heart left ventricle"
## 
## $samples[[1]]$organPart[[3]]
## [1] "heart right ventricle"
## 
## $samples[[1]]$organPart[[4]]
## [1] "interventricular septum"
## 
## $samples[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
## 
## $samples[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
## 
## 
## $samples[[1]]$disease
## $samples[[1]]$disease[[1]]
## NULL
## 
## 
## $samples[[1]]$preservationMethod
## $samples[[1]]$preservationMethod[[1]]
## NULL
## 
## 
## $samples[[1]]$source
## $samples[[1]]$source[[1]]
## [1] "specimen_from_organism"
## 
## 
## 
## 
## $specimens
## $specimens[[1]]
## $specimens[[1]]$id
## $specimens[[1]]$id[[1]]
## [1] "CBTM-361B_AX"
## 
## $specimens[[1]]$id[[2]]
## [1] "CBTM-361B_LA"
## 
## $specimens[[1]]$id[[3]]
## [1] "CBTM-361B_LV"
## 
## $specimens[[1]]$id[[4]]
## [1] "CBTM-361B_RV"
## 
## $specimens[[1]]$id[[5]]
## [1] "CBTM-362C_AX"
## 
## $specimens[[1]]$id[[6]]
## [1] "CBTM-362C_LA"
## 
## $specimens[[1]]$id[[7]]
## [1] "CBTM-362C_LV"
## 
## $specimens[[1]]$id[[8]]
## [1] "CBTM-362C_RA"
## 
## $specimens[[1]]$id[[9]]
## [1] "CBTM-362C_RV"
## 
## $specimens[[1]]$id[[10]]
## [1] "CBTM-362C_SP"
## 
## $specimens[[1]]$id[[11]]
## [1] "CBTM-364B_AX"
## 
## $specimens[[1]]$id[[12]]
## [1] "CBTM-364B_LA"
## 
## $specimens[[1]]$id[[13]]
## [1] "CBTM-364B_LV"
## 
## $specimens[[1]]$id[[14]]
## [1] "CBTM-364B_RA"
## 
## $specimens[[1]]$id[[15]]
## [1] "CBTM-364B_RV"
## 
## $specimens[[1]]$id[[16]]
## [1] "CBTM-364B_SP"
## 
## $specimens[[1]]$id[[17]]
## [1] "CBTM-386C_AX"
## 
## $specimens[[1]]$id[[18]]
## [1] "CBTM-386C_LA"
## 
## $specimens[[1]]$id[[19]]
## [1] "CBTM-386C_LV"
## 
## $specimens[[1]]$id[[20]]
## [1] "CBTM-386C_RA"
## 
## $specimens[[1]]$id[[21]]
## [1] "CBTM-386C_RV"
## 
## $specimens[[1]]$id[[22]]
## [1] "CBTM-386C_SP"
## 
## $specimens[[1]]$id[[23]]
## [1] "CBTM-390C_AX"
## 
## $specimens[[1]]$id[[24]]
## [1] "CBTM-390C_LA"
## 
## $specimens[[1]]$id[[25]]
## [1] "CBTM-390C_LV"
## 
## $specimens[[1]]$id[[26]]
## [1] "CBTM-390C_RA"
## 
## $specimens[[1]]$id[[27]]
## [1] "CBTM-390C_RV"
## 
## $specimens[[1]]$id[[28]]
## [1] "CBTM-390C_SP"
## 
## $specimens[[1]]$id[[29]]
## [1] "CBTM-417C_AX"
## 
## $specimens[[1]]$id[[30]]
## [1] "CBTM-417C_LA"
## 
## $specimens[[1]]$id[[31]]
## [1] "CBTM-417C_LV"
## 
## $specimens[[1]]$id[[32]]
## [1] "CBTM-417C_RA"
## 
## $specimens[[1]]$id[[33]]
## [1] "CBTM-417C_RV"
## 
## $specimens[[1]]$id[[34]]
## [1] "CBTM-417C_SP"
## 
## $specimens[[1]]$id[[35]]
## [1] "CBTM-423C_AX"
## 
## $specimens[[1]]$id[[36]]
## [1] "CBTM-423C_LA"
## 
## $specimens[[1]]$id[[37]]
## [1] "CBTM-423C_LV"
## 
## $specimens[[1]]$id[[38]]
## [1] "CBTM-423C_RA"
## 
## $specimens[[1]]$id[[39]]
## [1] "CBTM-423C_RV"
## 
## $specimens[[1]]$id[[40]]
## [1] "CBTM-423C_SP"
## 
## $specimens[[1]]$id[[41]]
## [1] "CBTM-473C_AX"
## 
## $specimens[[1]]$id[[42]]
## [1] "CBTM-473C_LA"
## 
## $specimens[[1]]$id[[43]]
## [1] "CBTM-473C_LV"
## 
## $specimens[[1]]$id[[44]]
## [1] "CBTM-473C_RA"
## 
## $specimens[[1]]$id[[45]]
## [1] "CBTM-473C_RV"
## 
## $specimens[[1]]$id[[46]]
## [1] "CBTM-473C_SP"
## 
## $specimens[[1]]$id[[47]]
## [1] "H0015_AX"
## 
## $specimens[[1]]$id[[48]]
## [1] "H0015_LA"
## 
## $specimens[[1]]$id[[49]]
## [1] "H0015_LV"
## 
## $specimens[[1]]$id[[50]]
## [1] "H0015_RA"
## 
## $specimens[[1]]$id[[51]]
## [1] "H0015_RV"
## 
## $specimens[[1]]$id[[52]]
## [1] "H0015_SP"
## 
## $specimens[[1]]$id[[53]]
## [1] "H0020_AX"
## 
## $specimens[[1]]$id[[54]]
## [1] "H0020_LA"
## 
## $specimens[[1]]$id[[55]]
## [1] "H0020_LV"
## 
## $specimens[[1]]$id[[56]]
## [1] "H0020_RA"
## 
## $specimens[[1]]$id[[57]]
## [1] "H0020_RV"
## 
## $specimens[[1]]$id[[58]]
## [1] "H0020_SP"
## 
## $specimens[[1]]$id[[59]]
## [1] "H0025_AX"
## 
## $specimens[[1]]$id[[60]]
## [1] "H0025_LA"
## 
## $specimens[[1]]$id[[61]]
## [1] "H0025_LV"
## 
## $specimens[[1]]$id[[62]]
## [1] "H0025_RA"
## 
## $specimens[[1]]$id[[63]]
## [1] "H0025_RV"
## 
## $specimens[[1]]$id[[64]]
## [1] "H0025_SP"
## 
## $specimens[[1]]$id[[65]]
## [1] "H0026_AX"
## 
## $specimens[[1]]$id[[66]]
## [1] "H0026_LA"
## 
## $specimens[[1]]$id[[67]]
## [1] "H0026_LV"
## 
## $specimens[[1]]$id[[68]]
## [1] "H0026_RA"
## 
## $specimens[[1]]$id[[69]]
## [1] "H0026_RV"
## 
## $specimens[[1]]$id[[70]]
## [1] "H0026_SP"
## 
## $specimens[[1]]$id[[71]]
## [1] "H0035_AX"
## 
## $specimens[[1]]$id[[72]]
## [1] "H0035_LA"
## 
## $specimens[[1]]$id[[73]]
## [1] "H0035_LV"
## 
## $specimens[[1]]$id[[74]]
## [1] "H0035_RA"
## 
## $specimens[[1]]$id[[75]]
## [1] "H0035_RV"
## 
## $specimens[[1]]$id[[76]]
## [1] "H0035_SP"
## 
## $specimens[[1]]$id[[77]]
## [1] "H0037_AX"
## 
## $specimens[[1]]$id[[78]]
## [1] "H0037_LA"
## 
## $specimens[[1]]$id[[79]]
## [1] "H0037_LV"
## 
## $specimens[[1]]$id[[80]]
## [1] "H0037_RA"
## 
## $specimens[[1]]$id[[81]]
## [1] "H0037_RV"
## 
## $specimens[[1]]$id[[82]]
## [1] "H0037_SP"
## 
## 
## $specimens[[1]]$organ
## $specimens[[1]]$organ[[1]]
## [1] "heart"
## 
## 
## $specimens[[1]]$organPart
## $specimens[[1]]$organPart[[1]]
## [1] "apex of heart"
## 
## $specimens[[1]]$organPart[[2]]
## [1] "heart left ventricle"
## 
## $specimens[[1]]$organPart[[3]]
## [1] "heart right ventricle"
## 
## $specimens[[1]]$organPart[[4]]
## [1] "interventricular septum"
## 
## $specimens[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
## 
## $specimens[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
## 
## 
## $specimens[[1]]$disease
## $specimens[[1]]$disease[[1]]
## NULL
## 
## 
## $specimens[[1]]$preservationMethod
## $specimens[[1]]$preservationMethod[[1]]
## NULL
## 
## 
## $specimens[[1]]$source
## $specimens[[1]]$source[[1]]
## [1] "specimen_from_organism"
## 
## 
## 
## 
## $cellLines
## list()
## 
## $donorOrganisms
## $donorOrganisms[[1]]
## $donorOrganisms[[1]]$id
## $donorOrganisms[[1]]$id[[1]]
## [1] "CBTM-361B"
## 
## $donorOrganisms[[1]]$id[[2]]
## [1] "CBTM-362C"
## 
## $donorOrganisms[[1]]$id[[3]]
## [1] "CBTM-364B"
## 
## $donorOrganisms[[1]]$id[[4]]
## [1] "CBTM-386C"
## 
## $donorOrganisms[[1]]$id[[5]]
## [1] "CBTM-390C"
## 
## $donorOrganisms[[1]]$id[[6]]
## [1] "CBTM-417C"
## 
## $donorOrganisms[[1]]$id[[7]]
## [1] "CBTM-423C"
## 
## $donorOrganisms[[1]]$id[[8]]
## [1] "CBTM-473C"
## 
## $donorOrganisms[[1]]$id[[9]]
## [1] "H0015"
## 
## $donorOrganisms[[1]]$id[[10]]
## [1] "H0020"
## 
## $donorOrganisms[[1]]$id[[11]]
## [1] "H0025"
## 
## $donorOrganisms[[1]]$id[[12]]
## [1] "H0026"
## 
## $donorOrganisms[[1]]$id[[13]]
## [1] "H0035"
## 
## $donorOrganisms[[1]]$id[[14]]
## [1] "H0037"
## 
## 
## $donorOrganisms[[1]]$donorCount
## [1] 14
## 
## $donorOrganisms[[1]]$developmentStage
## $donorOrganisms[[1]]$developmentStage[[1]]
## [1] "adult"
## 
## $donorOrganisms[[1]]$developmentStage[[2]]
## [1] "human adult stage"
## 
## 
## $donorOrganisms[[1]]$genusSpecies
## $donorOrganisms[[1]]$genusSpecies[[1]]
## [1] "Homo sapiens"
## 
## 
## $donorOrganisms[[1]]$organismAge
## $donorOrganisms[[1]]$organismAge[[1]]
## $donorOrganisms[[1]]$organismAge[[1]]$value
## [1] "40-45"
## 
## $donorOrganisms[[1]]$organismAge[[1]]$unit
## [1] "year"
## 
## 
## $donorOrganisms[[1]]$organismAge[[2]]
## $donorOrganisms[[1]]$organismAge[[2]]$value
## [1] "45-50"
## 
## $donorOrganisms[[1]]$organismAge[[2]]$unit
## [1] "year"
## 
## 
## $donorOrganisms[[1]]$organismAge[[3]]
## $donorOrganisms[[1]]$organismAge[[3]]$value
## [1] "50-55"
## 
## $donorOrganisms[[1]]$organismAge[[3]]$unit
## [1] "year"
## 
## 
## $donorOrganisms[[1]]$organismAge[[4]]
## $donorOrganisms[[1]]$organismAge[[4]]$value
## [1] "55-60"
## 
## $donorOrganisms[[1]]$organismAge[[4]]$unit
## [1] "year"
## 
## 
## $donorOrganisms[[1]]$organismAge[[5]]
## $donorOrganisms[[1]]$organismAge[[5]]$value
## [1] "60-65"
## 
## $donorOrganisms[[1]]$organismAge[[5]]$unit
## [1] "year"
## 
## 
## $donorOrganisms[[1]]$organismAge[[6]]
## $donorOrganisms[[1]]$organismAge[[6]]$value
## [1] "65-70"
## 
## $donorOrganisms[[1]]$organismAge[[6]]$unit
## [1] "year"
## 
## 
## $donorOrganisms[[1]]$organismAge[[7]]
## $donorOrganisms[[1]]$organismAge[[7]]$value
## [1] "70-75"
## 
## $donorOrganisms[[1]]$organismAge[[7]]$unit
## [1] "year"
## 
## 
## 
## $donorOrganisms[[1]]$organismAgeRange
## $donorOrganisms[[1]]$organismAgeRange[[1]]
## $donorOrganisms[[1]]$organismAgeRange[[1]]$gte
## [1] 1261440000
## 
## $donorOrganisms[[1]]$organismAgeRange[[1]]$lte
## [1] 1419120000
## 
## 
## $donorOrganisms[[1]]$organismAgeRange[[2]]
## $donorOrganisms[[1]]$organismAgeRange[[2]]$gte
## [1] 1419120000
## 
## $donorOrganisms[[1]]$organismAgeRange[[2]]$lte
## [1] 1576800000
## 
## 
## $donorOrganisms[[1]]$organismAgeRange[[3]]
## $donorOrganisms[[1]]$organismAgeRange[[3]]$gte
## [1] 1576800000
## 
## $donorOrganisms[[1]]$organismAgeRange[[3]]$lte
## [1] 1734480000
## 
## 
## $donorOrganisms[[1]]$organismAgeRange[[4]]
## $donorOrganisms[[1]]$organismAgeRange[[4]]$gte
## [1] 1734480000
## 
## $donorOrganisms[[1]]$organismAgeRange[[4]]$lte
## [1] 1892160000
## 
## 
## $donorOrganisms[[1]]$organismAgeRange[[5]]
## $donorOrganisms[[1]]$organismAgeRange[[5]]$gte
## [1] 1892160000
## 
## $donorOrganisms[[1]]$organismAgeRange[[5]]$lte
## [1] 2049840000
## 
## 
## $donorOrganisms[[1]]$organismAgeRange[[6]]
## $donorOrganisms[[1]]$organismAgeRange[[6]]$gte
## [1] 2049840000
## 
## $donorOrganisms[[1]]$organismAgeRange[[6]]$lte
## [1] 2207520000
## 
## 
## $donorOrganisms[[1]]$organismAgeRange[[7]]
## $donorOrganisms[[1]]$organismAgeRange[[7]]$gte
## [1] 2207520000
## 
## $donorOrganisms[[1]]$organismAgeRange[[7]]$lte
## [1] 2365200000
## 
## 
## 
## $donorOrganisms[[1]]$biologicalSex
## $donorOrganisms[[1]]$biologicalSex[[1]]
## [1] "female"
## 
## $donorOrganisms[[1]]$biologicalSex[[2]]
## [1] "male"
## 
## 
## $donorOrganisms[[1]]$disease
## $donorOrganisms[[1]]$disease[[1]]
## [1] "Diabetes"
## 
## $donorOrganisms[[1]]$disease[[2]]
## [1] "diabetes mellitus (disease)"
## 
## $donorOrganisms[[1]]$disease[[3]]
## [1] "hypertension"
## 
## $donorOrganisms[[1]]$disease[[4]]
## [1] "normal"
## 
## 
## 
## 
## $organoids
## list()
## 
## $cellSuspensions
## $cellSuspensions[[1]]
## $cellSuspensions[[1]]$organ
## $cellSuspensions[[1]]$organ[[1]]
## [1] "heart"
## 
## 
## $cellSuspensions[[1]]$organPart
## $cellSuspensions[[1]]$organPart[[1]]
## [1] "apex of heart"
## 
## $cellSuspensions[[1]]$organPart[[2]]
## [1] "heart left ventricle"
## 
## $cellSuspensions[[1]]$organPart[[3]]
## [1] "heart right ventricle"
## 
## $cellSuspensions[[1]]$organPart[[4]]
## [1] "interventricular septum"
## 
## $cellSuspensions[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
## 
## $cellSuspensions[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
## 
## 
## $cellSuspensions[[1]]$selectedCellType
## $cellSuspensions[[1]]$selectedCellType[[1]]
## NULL
## 
## 
## $cellSuspensions[[1]]$totalCells
## [1] 791000
## 
## 
## 
## $dates
## $dates[[1]]
## $dates[[1]]$aggregateLastModifiedDate
## [1] "2021-02-26T16:30:00.000000Z"
## 
## $dates[[1]]$aggregateSubmissionDate
## [1] "2020-07-22T12:26:56.289000Z"
## 
## $dates[[1]]$aggregateUpdateDate
## [1] "2021-02-26T16:30:00.000000Z"
## 
## $dates[[1]]$lastModifiedDate
## [1] "2020-10-19T16:31:10.620000Z"
## 
## $dates[[1]]$submissionDate
## [1] "2020-07-22T12:26:56.289000Z"
## 
## $dates[[1]]$updateDate
## [1] "2020-10-19T16:31:10.620000Z"
## 
## 
## 
## $fileTypeSummaries
## $fileTypeSummaries[[1]]
## $fileTypeSummaries[[1]]$count
## [1] 768
## 
## $fileTypeSummaries[[1]]$fileSource
## $fileTypeSummaries[[1]]$fileSource[[1]]
## NULL
## 
## 
## $fileTypeSummaries[[1]]$totalSize
## [1] 3.05423e+12
## 
## $fileTypeSummaries[[1]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[1]]$format
## [1] "fastq.gz"
## 
## $fileTypeSummaries[[1]]$isIntermediate
## NULL
## 
## $fileTypeSummaries[[1]]$contentDescription
## $fileTypeSummaries[[1]]$contentDescription[[1]]
## [1] "DNA sequence"
## 
## 
## 
## $fileTypeSummaries[[2]]
## $fileTypeSummaries[[2]]$count
## [1] 148
## 
## $fileTypeSummaries[[2]]$fileSource
## $fileTypeSummaries[[2]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[2]]$totalSize
## [1] 286860224345
## 
## $fileTypeSummaries[[2]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[2]]$format
## [1] "loom"
## 
## $fileTypeSummaries[[2]]$isIntermediate
## [1] TRUE
## 
## $fileTypeSummaries[[2]]$contentDescription
## $fileTypeSummaries[[2]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## 
## $fileTypeSummaries[[3]]
## $fileTypeSummaries[[3]]$count
## [1] 148
## 
## $fileTypeSummaries[[3]]$fileSource
## $fileTypeSummaries[[3]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[3]]$totalSize
## [1] 2.703466e+12
## 
## $fileTypeSummaries[[3]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[3]]$format
## [1] "bam"
## 
## $fileTypeSummaries[[3]]$isIntermediate
## NULL
## 
## $fileTypeSummaries[[3]]$contentDescription
## $fileTypeSummaries[[3]]$contentDescription[[1]]
## NULL
## 
## 
## 
## $fileTypeSummaries[[4]]
## $fileTypeSummaries[[4]]$count
## [1] 2
## 
## $fileTypeSummaries[[4]]$fileSource
## $fileTypeSummaries[[4]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[4]]$totalSize
## [1] 7653912940
## 
## $fileTypeSummaries[[4]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[4]]$format
## [1] "loom"
## 
## $fileTypeSummaries[[4]]$isIntermediate
## [1] FALSE
## 
## $fileTypeSummaries[[4]]$contentDescription
## $fileTypeSummaries[[4]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## 
## $fileTypeSummaries[[5]]
## $fileTypeSummaries[[5]]$count
## [1] 1
## 
## $fileTypeSummaries[[5]]$fileSource
## $fileTypeSummaries[[5]]$fileSource[[1]]
## [1] "Contributor"
## 
## 
## $fileTypeSummaries[[5]]$totalSize
## [1] 5068859764
## 
## $fileTypeSummaries[[5]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[5]]$format
## [1] "h5ad"
## 
## $fileTypeSummaries[[5]]$isIntermediate
## [1] FALSE
## 
## $fileTypeSummaries[[5]]$contentDescription
## $fileTypeSummaries[[5]]$contentDescription[[1]]
## [1] "Matrix"

9 Exploring manifest files

See the accompanying “Human Cell Atlas Manifests” vignette on details pertaining to the use of the manifest endpoint and further annotation of .loom files

10 Session info

sessionInfo()
## R version 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] httr_1.4.2                  hca_1.5.0                  
##  [3] LoomExperiment_1.15.0       BiocIO_1.7.0               
##  [5] rhdf5_2.41.0                SingleCellExperiment_1.19.0
##  [7] SummarizedExperiment_1.27.0 Biobase_2.57.0             
##  [9] GenomicRanges_1.49.0        GenomeInfoDb_1.33.0        
## [11] IRanges_2.31.0              S4Vectors_0.35.0           
## [13] BiocGenerics_0.43.0         MatrixGenerics_1.9.0       
## [15] matrixStats_0.62.0          dplyr_1.0.8                
## [17] BiocStyle_2.25.0           
## 
## loaded via a namespace (and not attached):
##  [1] tidyr_1.2.0            sass_0.4.1             vroom_1.5.7           
##  [4] bit64_4.0.5            jsonlite_1.8.0         bslib_0.3.1           
##  [7] assertthat_0.2.1       BiocManager_1.30.17    BiocFileCache_2.5.0   
## [10] blob_1.2.3             GenomeInfoDbData_1.2.8 yaml_2.3.5            
## [13] pillar_1.7.0           RSQLite_2.2.12         lattice_0.20-45       
## [16] glue_1.6.2             digest_0.6.29          XVector_0.37.0        
## [19] htmltools_0.5.2        Matrix_1.4-1           pkgconfig_2.0.3       
## [22] bookdown_0.26          zlibbioc_1.43.0        purrr_0.3.4           
## [25] HDF5Array_1.25.0       tzdb_0.3.0             tibble_3.1.6          
## [28] generics_0.1.2         ellipsis_0.3.2         withr_2.5.0           
## [31] cachem_1.0.6           cli_3.3.0              magrittr_2.0.3        
## [34] crayon_1.5.1           memoise_2.0.1          evaluate_0.15         
## [37] fansi_1.0.3            tools_4.2.0            hms_1.1.1             
## [40] formatR_1.12           lifecycle_1.0.1        stringr_1.4.0         
## [43] Rhdf5lib_1.19.0        DelayedArray_0.23.0    lambda.r_1.2.4        
## [46] compiler_4.2.0         jquerylib_0.1.4        rlang_1.0.2           
## [49] futile.logger_1.4.3    grid_4.2.0             RCurl_1.98-1.6        
## [52] rhdf5filters_1.9.0     rappdirs_0.3.3         bitops_1.0-7          
## [55] rmarkdown_2.14         DBI_1.1.2              curl_4.3.2            
## [58] R6_2.5.1               knitr_1.38             fastmap_1.1.0         
## [61] bit_4.0.4              utf8_1.2.2             filelock_1.0.2        
## [64] futile.options_1.0.1   readr_2.1.2            stringi_1.7.6         
## [67] parallel_4.2.0         Rcpp_1.0.8.3           vctrs_0.4.1           
## [70] dbplyr_2.1.1           tidyselect_1.1.2       xfun_0.30