SeqSQC
This package is for version 3.9 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: 3.9
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 "3.6") 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 | 1.6.0 |
| 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_1.6.0.tar.gz |
| Windows Binary | SeqSQC_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | SeqSQC_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SeqSQC |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |