SeqSQC
This package is for version 3.15 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: 3.15
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 "4.2") 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 | ||
NEWS | Text |
Details
biocViews | Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software |
Version | 1.18.0 |
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 |
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_1.18.0.tar.gz |
Windows Binary | SeqSQC_1.18.0.zip |
macOS Binary (x86_64) | SeqSQC_1.18.0.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 |
Old Source Packages for BioC 3.15 | Source Archive |