concordexR

Calculate the concordex coefficient

Bioconductor version: Release (3.17)

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 "4.3") and enter:

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

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	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	BiocParallel, cli, DelayedArray, ggplot2, Matrix, methods, pheatmap, rlang, scales
Linking To
Suggests	BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr
System Requirements
Enhances
URL	https://github.com/pachterlab/concordexR https://pachterlab.github.io/concordexR/
Bug Reports	https://github.com/pachterlab/concordexR/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	concordexR_1.0.0.tar.gz
Windows Binary	concordexR_1.0.0.zip
macOS Binary (x86_64)	concordexR_1.0.0.tgz
macOS Binary (arm64)	concordexR_1.0.0.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