dearseq
This is thereleased version of dearseq; for the devel version, seedearseq.
Differential Expression Analysis for RNA-seq data through a robust variance component test
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-0646-452X, 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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("dearseq")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | GPL-2 | fileLICENSE |
| 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 | |
| Suggests Me | GeoTcgaData,TcGSA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | dearseq_1.22.0.tar.gz |
| Windows Binary (x86_64) | dearseq_1.22.0.zip |
| macOS Binary (x86_64) | dearseq_1.22.0.tgz |
| macOS Binary (arm64) | dearseq_1.22.0.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 |