dearseq

This package is for version 3.11 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: 3.11

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 (!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")
dearseqUserguide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BiomedicalInformatics, CellBiology, DNASeq, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-2 | file LICENSE
Depends R (>= 3.6.0)
Imports CompQuadForm, ggplot2, KernSmooth, matrixStats, methods, parallel, pbapply, stats, statmod
System Requirements
URL
Bug Reports https://github.com/borishejblum/dearseq/issues
See More
Suggests Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr
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Build Report Build Report

Package Archives

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

Source Package dearseq_1.0.0.tar.gz
Windows Binary dearseq_1.0.0.zip
macOS 10.13 (High Sierra) dearseq_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dearseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dearseq
Bioc Package Browser https://code.bioconductor.org/browse/dearseq/
Package Short Url https://bioconductor.org/packages/dearseq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive