DOI: 10.18129/B9.bioc.dearseq    

This package is for version 3.15 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: 3.15

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>

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biocViews BiomedicalInformatics, CellBiology, DNASeq, DifferentialExpression, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version 1.8.4
In Bioconductor since BioC 3.11 (R-4.0) (2.5 years)
License GPL-2 | file LICENSE
Depends R (>= 3.6.0)
Imports CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, stats, statmod, survey, tibble, viridisLite
Suggests Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr
Depends On Me
Imports Me benchdamic
Suggests Me GeoTcgaData, TcGSA
Links To Me
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