simpleSingleCell
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Bioconductor version: Release (3.19)
Once a proud workflow package, this is now a shell of its former self. Almost all of its content has been cannibalized for use in the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained as reminders of the glory that once was, also providing redirection for existing external links to the relevant OSCA book chapters.
Author: Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("simpleSingleCell")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simpleSingleCell")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("simpleSingleCell")
01. Introduction | HTML | |
02. Read count data | HTML | |
03. UMI count data | HTML | |
04. Droplet-based data | HTML | |
05. Correcting batch effects | HTML | |
06. Quality control details | HTML | |
07. Spike-in normalization | HTML | |
08. Detecting doublets | HTML | |
09. Advanced variance modelling | HTML | |
10. Detecting differential expression | HTML | |
11. Advanced batch correction | HTML | |
12. Scalability for big data | HTML | |
13. Further analysis strategies | HTML | R Script |
Details
biocViews | ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow |
Version | 1.28.0 |
License | Artistic-2.0 |
Depends | |
Imports | utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle |
System Requirements | |
URL | https://www.bioconductor.org/help/workflows/simpleSingleCell/ |
See More
Suggests | readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache, org.Mm.eg.db |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | simpleSingleCell_1.28.0.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/simpleSingleCell |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/simpleSingleCell |
Package Short Url | https://bioconductor.org/packages/simpleSingleCell/ |
Package Downloads Report | Download Stats |