dearseq
This package is for version 3.16 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: 3.16
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("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")| dearseqUserguide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, DNASeq, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics |
| Version | 1.10.0 |
| 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 | TcGSA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dearseq_1.10.0.tar.gz |
| Windows Binary | dearseq_1.10.0.zip |
| macOS Binary (x86_64) | dearseq_1.10.0.tgz |
| macOS Binary (arm64) | dearseq_1.10.0.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 3.16 | Source Archive |