DCATS

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

Differential Composition Analysis Transformed by a Similarity matrix

Bioconductor version: Development (3.21)

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] (ORCID: ), Chuen Chau [aut], Yuanhua Huang [aut], Joshua W.K. Ho [aut]

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

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

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Normalization, SingleCell, Software
Version	1.5.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.1.0), stats
Imports	MCMCpack, matrixStats, robustbase, aod, e1071
System Requirements
URL

Suggests	testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle
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Build Report	Build Report

Package Archives

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

Source Package	DCATS_1.5.0.tar.gz
Windows Binary (x86_64)	DCATS_1.5.0.zip
macOS Binary (x86_64)	DCATS_1.5.0.tgz
macOS Binary (arm64)
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