This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

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 (3.18)

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 "4.3") 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 1.9.0
License GPL-3 + file LICENSE
Depends R (>= 4.3.0), SingleCellExperiment, SpatialExperiment, cytomapper
Imports methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array
Linking To
Suggests BiocStyle, knitr, rmarkdown, markdown, testthat
System Requirements
Enhances
URL https://github.com/BodenmillerGroup/imcdatasets
Bug Reports https://github.com/BodenmillerGroup/imcdatasets/issues
See More
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_1.9.0.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