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("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 | ||
| 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 |
| 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 | concordexR_1.3.0.tar.gz |
| Windows Binary | concordexR_1.3.0.zip (64-bit only) |
| 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 |