Package: SeqSQC 1.29.0

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_1.29.0.tar.gz
SeqSQC_1.29.0.zip(r-4.5)SeqSQC_1.29.0.zip(r-4.4)SeqSQC_1.29.0.zip(r-4.3)
SeqSQC_1.29.0.tgz(r-4.5-any)SeqSQC_1.29.0.tgz(r-4.4-any)SeqSQC_1.29.0.tgz(r-4.3-any)
SeqSQC_1.29.0.tar.gz(r-4.5-noble)SeqSQC_1.29.0.tar.gz(r-4.4-noble)
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SeqSQC.pdf |SeqSQC.html✨
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-1.29.0(bioc 3.21)SeqSQC-1.28.0(bioc 3.20)

experiment datahomo_sapiens_datasequencing dataproject1000genomesgenome

5.26 score 2 scripts 346 downloads 2 mentions 17 exports 111 dependencies

Last updated 5 months agofrom:42fdfb6802. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 25 2025
R-4.5-winWARNINGMar 25 2025
R-4.5-macWARNINGMar 25 2025
R-4.5-linuxWARNINGMar 25 2025
R-4.4-winWARNINGMar 25 2025
R-4.4-macWARNINGMar 25 2025
R-4.4-linuxWARNINGMar 25 2025
R-4.3-winWARNINGMar 25 2025
R-4.3-macWARNINGMar 25 2025

Exports:gdsfilegdsfile<-IBDCheckIBDRemoveInbreedingLoadVfileMissingRatePCACheckplotQCproblemListQCresultQCresult<-RenderReportsampleQCSeqOpenSeqSQCSexCheck

Dependencies:AnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemclassclicolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdplyre1071evaluateExperimentHubfansifarverfastmapfilelockfontawesomeforcatsfsgdsfmtgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggplot2ggstatsgluegtablehighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplotlyplyrpngprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownRSQLiteS4VectorssassscalesSNPRelatestringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryaml

Sample Quality Check for NGS Data using SeqSQC package

Qian Liu, Qianqian Zhu

Rendered fromvignette.Rmdusingknitr::rmarkdownon Mar 25 2025.

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