Package: qsvaR 1.11.1

Hedia Tnani

qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.

Authors:Joshua Stolz [aut], Hedia Tnani [ctb, cre], Leonardo Collado-Torres [ctb], Nicholas J. Eagles [aut]

qsvaR_1.11.1.tar.gz
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qsvaR.pdf |qsvaR.html✨
qsvaR/json (API)
NEWS

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

Bug tracker:https://github.com/lieberinstitute/qsvar/issues

Datasets:

On BioConductor:qsvaR-1.11.1(bioc 3.21)qsvaR-1.10.0(bioc 3.20)

softwareworkflowstepnormalizationbiologicalquestiondifferentialexpressionsequencingcoveragebioconductorbraindegradationhumanqsva

5.26 score 4 scripts 350 downloads 9 exports 87 dependencies

Last updated 4 months agofrom:55f85137fa. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 11 2025
R-4.5-winNOTEMar 11 2025
R-4.5-macNOTEMar 11 2025
R-4.5-linuxNOTEMar 11 2025
R-4.4-winNOTEMar 11 2025
R-4.4-macNOTEMar 11 2025
R-4.4-linuxNOTEMar 11 2025
R-4.3-winNOTEMar 11 2025
R-4.3-macNOTEMar 11 2025

Exports:DEqualget_qsvsgetDegTxgetPCsk_qsvsnormalize_tx_namesqSVAselect_transcriptswhich_tx_names

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydplyredgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerrlangRSQLiteS4ArraysS4VectorsscalessnowSparseArraystatmodSummarizedExperimentsurvivalsvasystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVector

Introduction to qsvaR

Joshua M. Stolz, Hedia Tnani, Leonardo Collado-Torres

Rendered fromIntro_qsvaR.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2024-11-26
Started: 2021-12-14