dearseq

DOI: 10.18129/B9.bioc.dearseq    

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

Bioconductor version: Release (3.15)

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], Mélanie Huchon [ctb]

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

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

Installation

To install this package, start R (version "4.2") 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 1.8.4
In Bioconductor since BioC 3.11 (R-4.0) (2.5 years)
License GPL-2 | file LICENSE
Depends R (>= 3.6.0)
Imports CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, stats, statmod, survey, tibble, 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 benchdamic
Suggests Me GeoTcgaData, TcGSA
Links To Me
Build Report  

Package Archives

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

Source Package dearseq_1.8.4.tar.gz
Windows Binary dearseq_1.8.4.zip
macOS Binary (x86_64) dearseq_1.8.4.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
Old Source Packages for BioC 3.15 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: