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dearseq

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

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

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

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 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-2 | file LICENSE
Depends R (>= 3.6.0)
Imports CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite
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
Linking To
Enhances
Depends On Me
Imports Me benchdamic
Suggests Me GeoTcgaData
Links To Me
Build Report Build Report

Package Archives

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

Source Package dearseq_1.15.0.tar.gz
Windows Binary dearseq_1.15.0.zip
macOS Binary (x86_64) dearseq_1.15.0.tgz
macOS Binary (arm64) dearseq_1.15.0.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