imcdatasets
Collection of publicly available imaging mass cytometry (IMC) datasets
Bioconductor version: Release (3.19)
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("imcdatasets")
):
Installation
To install this package, start R (version "4.4") 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")
Accessing IMC datasets | HTML | R Script |
Contributing guidelines and datasets format | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, ImmunoOncologyData, PackageTypeData, ReproducibleResearch, SingleCellData, SpatialData, TechnologyData, Tissue |
Version | 1.12.0 |
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 |
See More
Suggests | BiocStyle, knitr, rmarkdown, markdown, testthat |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | imcdatasets_1.12.0.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 |