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concordexR

This is the development version of concordexR; for the stable release version, see concordexR.

Calculate the concordex coefficient


Bioconductor version: Development (3.19)

Many analysis workflows include approximation of a nearest neighbors graph followed by clustering of the graph structure. The concordex coefficient estimates the concordance between the graph and clustering results. The package 'concordexR' is an R implementation of the original concordex Python-based command line tool.

Author: Kayla Jackson [aut, cre] , A. Sina Booeshaghi [aut] , Angel Galvez-Merchan [aut] , Lambda Moses [aut] , Laura Luebbert [ctb] , Lior Pachter [aut, rev, ths]

Maintainer: Kayla Jackson <kaylajac at caltech.edu>

Citation (from within R, enter citation("concordexR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("concordexR")

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("concordexR")
concordex-demo HTML R Script
overview HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GraphAndNetwork, SingleCell, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.2)
Imports BiocParallel, cli, DelayedArray, ggplot2, Matrix, methods, pheatmap, rlang, scales
System Requirements
URL https://github.com/pachterlab/concordexR https://pachterlab.github.io/concordexR/
Bug Reports https://github.com/pachterlab/concordexR/issues
See More
Suggests BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package concordexR_1.3.0.tar.gz
Windows Binary concordexR_1.3.0.zip
macOS Binary (x86_64) concordexR_1.3.0.tgz
macOS Binary (arm64) concordexR_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/concordexR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/concordexR
Bioc Package Browser https://code.bioconductor.org/browse/concordexR/
Package Short Url https://bioconductor.org/packages/concordexR/
Package Downloads Report Download Stats