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:
Maintainer: Nicolas Damond <nicolas.damond at dqbm.uzh.ch>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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_1.15.0.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 [email protected]:packages/imcdatasets |
| Package Short Url | https://bioconductor.org/packages/imcdatasets/ |
| Package Downloads Report | Download Stats |