dearseq

DOI: 10.18129/B9.bioc.dearseq    

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

Bioconductor version: Release (3.12)

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: 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 Gauthier M, Agniel D, ThiƩbaut R & Hejblum BP (2019). dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, *bioRxiv* 635714.

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

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 "4.0") and enter:

if (!requireNamespace("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")

 

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Details

biocViews BiomedicalInformatics, CellBiology, DNASeq, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.11 (R-4.0) (0.5 years)
License GPL-2 | file LICENSE
Depends R (>= 3.6.0)
Imports CompQuadForm, ggplot2, KernSmooth, matrixStats, methods, parallel, pbapply, stats, statmod
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
Links To Me
Build Report  

Package Archives

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

Source Package dearseq_1.2.0.tar.gz
Windows Binary dearseq_1.2.0.zip
macOS 10.13 (High Sierra) dearseq_1.2.0.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

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