To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

SeqSQC

DOI: 10.18129/B9.bioc.SeqSQC    

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

Bioconductor version: Release (3.6)

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:

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

Documentation

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 1.0.0
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
Build Report  

Package Archives

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

Source Package SeqSQC_1.0.0.tar.gz
Windows Binary SeqSQC_1.0.0.zip
Mac OS X 10.11 (El Capitan) SeqSQC_1.0.0.tgz
Source Repository git clone https://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: