imcdatasets
This is the released version of imcdatasets; for the devel version, see imcdatasets.
Collection of publicly available imaging mass cytometry (IMC) datasets
Bioconductor version: Release (3.23)
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]
, Nathan Steenbuck [aut, cre]
, Nils Eling [ctb]
, Fischer Jana [ctb]
Maintainer: Nathan Steenbuck <nathan.steenbuck at uzh.ch>
citation("imcdatasets")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.20.1 |
| 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 | OSTA |
| 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_1.20.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |