imcdatasets

DOI: 10.18129/B9.bioc.imcdatasets  

Collection of publicly available imaging mass cytometry (IMC) datasets

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, ImmunoOncologyData, PackageTypeData, ReproducibleResearch, SingleCellData, SpatialData, TechnologyData, Tissue
Version	1.8.0
License	GPL-3 + file LICENSE
Depends	R (>= 4.3.0), SingleCellExperiment, SpatialExperiment, cytomapper
Imports	methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, markdown, testthat
SystemRequirements
Enhances
URL	https://github.com/BodenmillerGroup/imcdatasets
BugReports	https://github.com/BodenmillerGroup/imcdatasets/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	imcdatasets_1.8.0.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/
Package Downloads Report	Download Stats