SeqSQC

This package is for version 3.6 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: 3.6

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 (version "3.4") 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

Reference Manual PDF
NEWS Text

Details

biocViews Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software
Version 1.0.0
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
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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
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqSQC
Package Short Url https://bioconductor.org/packages/SeqSQC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive