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 (3.21)

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] (ORCID: ), Nils Eling [ctb] (ORCID: ), Fischer Jana [ctb] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, ImmunoOncologyData, PackageTypeData, ReproducibleResearch, SingleCellData, SpatialData, TechnologyData, Tissue
Version	1.15.0
License	GPL-3 + file LICENSE
Depends	R (>= 4.4.0), 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

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

Package Archives

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

Source Package	imcdatasets_1.15.0.tar.gz
Windows Binary (x86_64)
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