SeqSQC

DOI: 10.18129/B9.bioc.SeqSQC    

This package is for version 3.7 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: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SeqSQC")

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	1.2.0
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
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_1.2.0.tar.gz
Windows Binary	SeqSQC_1.2.0.zip
Mac OS X 10.11 (El Capitan)	SeqSQC_1.2.0.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