imcdatasets

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Collection of publicly available imaging mass cytometry (IMC) datasets

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-3027-8989 , Nathan Steenbuck [aut, cre] ORCID: 0000-0003-2712-5359 , Nils Eling [ctb] ORCID: 0000-0002-4711-1176 , Fischer Jana [ctb] ORCID: 0000-0001-9047-8400

Maintainer: Nathan Steenbuck <nathan.steenbuck at uzh.ch>

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

Nicolas Damond, Nathan Steenbuck. imcdatasets: Collection of publicly available imaging mass cytometry (IMC) datasets. doi:10.18129/B9.bioc.imcdatasets, R package version 1.21.3, https://bioconductor.org/packages/imcdatasets.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, ImmunoOncologyData, PackageTypeData, ReproducibleResearch, SingleCellData, SpatialData, TechnologyData, Tissue
Version	1.21.3
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.6.0), SingleCellExperiment, SpatialExperiment, cytomapper
Imports	methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array
System Requirements
URL	https://github.com/BodenmillerGroup/imcdatasets https://bodenmillergroup.github.io/imcdatasets/
Bug Reports	https://github.com/BodenmillerGroup/imcdatasets/issues

Suggests	BiocStyle, knitr, rmarkdown, markdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	imcdatasets_1.21.3.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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