Package: dearseq 1.17.0

Boris P. Hejblum

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

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.

Authors:Denis Agniel [aut], Boris P. Hejblum [aut, cre], Marine Gauthier [aut], Mélanie Huchon [ctb]

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dearseq.pdf |dearseq.html✨
dearseq/json (API)
NEWS

# Install 'dearseq' in R:
install.packages('dearseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/borishejblum/dearseq/issues

Datasets:
  • PBT_gmt - PBT gene sets related to kidney transplant
  • baduel_gmt - Small portion of RNA-seq data from plant physiology study.
  • design - Small portion of RNA-seq data from plant physiology study.
  • expr_norm_corr - Small portion of RNA-seq data from plant physiology study.

On BioConductor:dearseq-1.17.0(bioc 3.20)dearseq-1.16.0(bioc 3.19)

bioconductor-package

15 exports 1.38 score 50 dependencies 1 dependents

Last updated 2 months agofrom:07913161c7

Exports:dear_seqdgsa_seqpermPvalsplot_hist_pvalsplot_ord_pvalsplot_weightssp_weightsspaghettiPlot1GSvc_scorevc_score_hvc_score_h_permvc_score_permvc_test_asymvc_test_permvoom_weights

Dependencies:clicolorspaceCompQuadFormDBIdplyrfansifarvergenericsggplot2gluegtableisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvminqamitoolsmunsellnlmenumDerivpatchworkpbapplypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangscalesscattermorestatmodstringistringrsurveysurvivaltibbletidyselectutf8vctrsviridisLitewithr

User guide to the dearseq R package

Marine Gauthier, Denis Agniel, Boris Hejblum

Rendered fromdearseqUserguide.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-02-01
Started: 2019-05-16