SeqSQC

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


Bioconductor version: Release (3.19)

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 "4.4") 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

To view documentation for the version of this package installed in your system, start R and enter:

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

Details

biocViews Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.4), ExperimentHub(>= 1.3.7), SNPRelate(>= 1.10.2)
Imports e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils
System Requirements
URL https://github.com/Liubuntu/SeqSQC
Bug Reports https://github.com/Liubuntu/SeqSQC/issues
See More
Suggests BiocStyle, knitr, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SeqSQC_1.26.0.tar.gz
Windows Binary SeqSQC_1.26.0.zip (64-bit only)
macOS Binary (x86_64) SeqSQC_1.26.0.tgz
macOS Binary (arm64) SeqSQC_1.26.0.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