Package: SeqSQC 1.34.0

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_1.34.0.tar.gz
SeqSQC_1.34.0.zip(r-4.7)SeqSQC_1.34.0.zip(r-4.6)SeqSQC_1.34.0.zip(r-4.5)
SeqSQC_1.34.0.tgz(r-4.6-any)SeqSQC_1.34.0.tgz(r-4.5-any)
SeqSQC_1.34.0.tar.gz(r-4.7-any)SeqSQC_1.34.0.tar.gz(r-4.6-any)
SeqSQC_1.34.0.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-release.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 380 downloads 2 mentions 17 exports 106 dependencies

Last updated from:eec2d71167 (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING175
linux-devel-x86_64WARNING543
source / vignettesOK360
linux-release-x86_64WARNING343
macos-release-arm64WARNING536
macos-oldrel-arm64WARNING153
windows-develWARNING666
windows-releaseWARNING240
windows-oldrelWARNING742
wasm-releaseOK152

Exports:gdsfilegdsfile<-IBDCheckIBDRemoveInbreedingLoadVfileMissingRatePCACheckplotQCproblemListQCresultQCresult<-RenderReportsampleQCSeqOpenSeqSQCSexCheck

Dependencies:AnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemclassclicpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdplyre1071evaluateExperimentHubfarverfastmapfilelockfontawesomeforcatsfsgdsfmtgenericsGenomicRangesGGallyggplot2ggstatsgluegtablehighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlazyevallifecyclemagrittrMASSmemoisemimeopensslotelpatchworkpillarpkgconfigplotlyplyrpngprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppreshape2RhpcBLASctlrlangrmarkdownRSQLiteS4VectorsS7sassscalesSeqinfoSNPRelatestringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

Sample Quality Check for NGS Data using SeqSQC package

Qian Liu, Qianqian Zhu

Rendered fromvignette.Rmdusingknitr::rmarkdownon May 30 2026.

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