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SeqSQC

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


Bioconductor version: Release (3.18)

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 buffalo.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SeqSQC")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SeqSQC")
Sample Quality Check for Next-Generation Sequencing Data with SeqSQC HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
System Requirements
URL https://github.com/Liubuntu/SeqSQC
Bug Reports https://github.com/Liubuntu/SeqSQC/issues
See More
Suggests BiocStyle, knitr, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SeqSQC_1.24.0.tar.gz
Windows Binary SeqSQC_1.24.0.zip (64-bit only)
macOS Binary (x86_64) SeqSQC_1.24.0.tgz
macOS Binary (arm64) SeqSQC_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SeqSQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqSQC
Bioc Package Browser https://code.bioconductor.org/browse/SeqSQC/
Package Short Url https://bioconductor.org/packages/SeqSQC/
Package Downloads Report Download Stats