DOI: 10.18129/B9.bioc.SeqSQC  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SeqSQC.

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

Bioconductor version: 3.16

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

Author: Qian Liu [aut, cre]

Maintainer: Qian Liu <qliu7 at>

Citation (from within R, enter citation("SeqSQC")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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HTML R Script Sample Quality Check for Next-Generation Sequencing Data with SeqSQC
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biocViews Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL-3
Depends R (>= 3.4), ExperimentHub(>= 1.3.7), SNPRelate(>= 1.10.2)
Imports e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils
Suggests BiocStyle, knitr, testthat
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