DCATS

DOI: 10.18129/B9.bioc.DCATS  

Differential Composition Analysis Transformed by a Similarity matrix

Bioconductor version: Release (3.18)

Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.

Author: Xinyi Lin [aut, cre] , Chuen Chau [aut], Yuanhua Huang [aut], Joshua W.K. Ho [aut]

Maintainer: Xinyi Lin <linxy29 at connect.hku.hk>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("DCATS")

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("DCATS")

 

HTML	R Script	Differential Composition Analysis with DCATS
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Normalization, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), stats
Imports	MCMCpack, matrixStats, robustbase, aod, e1071
LinkingTo
Suggests	testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
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	DCATS_1.0.0.tar.gz
Windows Binary	DCATS_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	DCATS_1.0.0.tgz
macOS Binary (arm64)	DCATS_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DCATS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DCATS
Bioc Package Browser	https://code.bioconductor.org/browse/DCATS/
Package Short Url	https://bioconductor.org/packages/DCATS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive