Package: SeqSQC 1.35.0

Qian Liu

SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

Authors:Qian Liu [aut, cre]

SeqSQC_1.35.0.tar.gz
SeqSQC_1.35.0.zip(r-4.7)SeqSQC_1.35.0.zip(r-4.6)SeqSQC_1.35.0.zip(r-4.5)
SeqSQC_1.35.0.tgz(r-4.6-any)SeqSQC_1.35.0.tgz(r-4.5-any)
SeqSQC_1.35.0.tar.gz(r-4.7-any)SeqSQC_1.35.0.tar.gz(r-4.6-any)
SeqSQC_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SeqSQC/json (API)
NEWS

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

Bug tracker:https://github.com/liubuntu/seqsqc/issues

On BioConductor:SeqSQC-1.35.0(bioc 3.24)SeqSQC-1.34.0(bioc 3.23)

experiment datahomo_sapiens_datasequencing dataproject1000genomesgenome

5.08 score 2 scripts 400 downloads 2 mentions 17 exports 106 dependencies

Last updated from:d08f6591c9. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING189
linux-devel-x86_64WARNING352
source / vignettesOK291
linux-release-x86_64WARNING329
macos-release-arm64WARNING209
macos-oldrel-arm64WARNING203
windows-develWARNING262
windows-releaseWARNING236
windows-oldrelWARNING235
wasm-releaseOK140

Exports:gdsfilegdsfile<-IBDCheckIBDRemoveInbreedingLoadVfileMissingRatePCACheckplotQCproblemListQCresultQCresult<-RenderReportsampleQCSeqOpenSeqSQCSexCheck

Dependencies:AnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemclassclicpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdplyre1071evaluateExperimentHubfarverfastmapfilelockfontawesomeforcatsfsgdsfmtgenericsGenomicRangesGGallyggplot2ggstatsgluegtablehighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlazyevallifecyclemagrittrMASSmemoisemimeopensslotelpatchworkpillarpkgconfigplotlyplyrpngprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppreshape2RhpcBLASctlrlangrmarkdownRSQLiteS4VectorsS7sassscalesSeqinfoSNPRelatestringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Sample Quality Check for NGS Data using SeqSQC package

Qian Liu, Qianqian Zhu

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2018-08-30
Started: 2017-08-24