dearseq

DOI: 10.18129/B9.bioc.dearseq    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see dearseq.

Differential Expression Analysis for RNA-seq data through a robust variance component test

Bioconductor version: 3.14

Differential Expression Analysis RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data. Methods are detailed in: i) Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020) dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics, 2(4):lqaa093.

Author: Denis Agniel [aut], Boris P. Hejblum [aut, cre], Marine Gauthier [aut]

Maintainer: Boris P. Hejblum <boris.hejblum at u-bordeaux.fr>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("dearseq")

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("dearseq")

 

HTML	R Script	dearseqUserguide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, CellBiology, DNASeq, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	GPL-2 | file LICENSE
Depends	R (>= 3.6.0)
Imports	ggplot2, KernSmooth, matrixStats, methods, patchwork, parallel, pbapply, stats, statmod, survey, viridisLite
LinkingTo
Suggests	Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr
SystemRequirements
Enhances
URL
BugReports	https://github.com/borishejblum/dearseq/issues
Depends On Me
Imports Me
Suggests Me	TcGSA
Links To Me
Build Report

Package Archives

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

Source Package	dearseq_1.6.0.tar.gz
Windows Binary	dearseq_1.6.0.zip
macOS 10.13 (High Sierra)	dearseq_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dearseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dearseq
Package Short Url	https://bioconductor.org/packages/dearseq/
Package Downloads Report	Download Stats