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imcdatasets

This is the development version of imcdatasets; for the stable release version, see imcdatasets.

Collection of publicly available imaging mass cytometry (IMC) datasets


Bioconductor version: Development (3.19)

The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.

Author: Nicolas Damond [aut, cre] , Nils Eling [ctb] , Fischer Jana [ctb]

Maintainer: Nicolas Damond <nicolas.damond at dqbm.uzh.ch>

Citation (from within R, enter citation("imcdatasets")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("imcdatasets")

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("imcdatasets")
Accessing IMC datasets HTML R Script
Contributing guidelines and datasets format HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, ImmunoOncologyData, PackageTypeData, ReproducibleResearch, SingleCellData, SpatialData, TechnologyData, Tissue
Version 1.11.0
License GPL-3 + file LICENSE
Depends R (>= 4.3.0), SingleCellExperiment, SpatialExperiment, cytomapper
Imports methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array
System Requirements
URL https://github.com/BodenmillerGroup/imcdatasets
Bug Reports https://github.com/BodenmillerGroup/imcdatasets/issues
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Suggests BiocStyle, knitr, rmarkdown, markdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package imcdatasets_1.11.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/imcdatasets
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/imcdatasets
Package Short Url https://bioconductor.org/packages/imcdatasets/
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