Bioconductor version: Release (3.15)
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")
):
To install this package, start R (version "4.2") 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.
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 |
Reference Manual | ||
Text | NEWS |
biocViews | ExperimentData, ExperimentHub, PackageTypeData, SingleCellData, TechnologyData, Tissue |
Version | 1.4.1 |
License | GPL-3 |
Depends | R (>= 4.2), SingleCellExperiment, 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 |
Follow Installation instructions to use this package in your R session.
Source Package | imcdatasets_1.4.1.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | |
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 |
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