SeqSQC

DOI: 10.18129/B9.bioc.SeqSQC    

This is the development version of SeqSQC; for the stable release version, see SeqSQC.

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

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SeqSQC", version = "devel")

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 1.3.1
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_1.3.1.tar.gz
Windows Binary SeqSQC_1.3.1.zip
Mac OS X 10.11 (El Capitan) SeqSQC_1.3.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/SeqSQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqSQC
Package Short Url http://bioconductor.org/packages/SeqSQC/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: