SeqSQC

DOI: 10.18129/B9.bioc.SeqSQC  

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

Bioconductor version: Release (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 buffalo.edu>

Installation

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

 

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

Details

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
LinkingTo
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL	https://github.com/Liubuntu/SeqSQC
BugReports	https://github.com/Liubuntu/SeqSQC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SeqSQC_1.20.0.tar.gz
Windows Binary	SeqSQC_1.20.0.zip
macOS Binary (x86_64)	SeqSQC_1.20.0.tgz
macOS Binary (arm64)	SeqSQC_1.20.0.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