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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, DNASeq, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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, TcGSA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dearseq_1.25.0.tar.gz |
| Windows Binary (x86_64) | dearseq_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | dearseq_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | dearseq_1.25.0.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 |