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Bioconductor - SeqSQC (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.31.0 In Bioconductor since BioC 3.6 (R-3.4) (7.5 years) License GPL-3 Depends R (>= 3.4), ExperimentHub(>= 1.3.7), SNPRelate(>= 1.10.2) Imports e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, 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 Package Archives

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

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