SeqSQC
A bioconductor package for sample quality check with next generation sequencing data
Bioconductor version: 3.23 · Package version: 1.34.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SeqSQC")Details
| Maintainer | Qian Liu <qliu7@buffalo.edu> |
| Author | Qian Liu [aut, cre] |
| License | GPL-3 |
| URL | https://github.com/Liubuntu/SeqSQC |
| Bug Reports | https://github.com/Liubuntu/SeqSQC/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software |
| Package Short Url | https://bioconductor.org/packages/SeqSQC/ |
Citation
From within R, enter citation("SeqSQC"):
Qian Liu. SeqSQC: A bioconductor package for sample quality check with next generation sequencing data. doi:10.18129/B9.bioc.SeqSQC, R package version 1.34.0, https://bioconductor.org/packages/SeqSQC.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SeqSQC_1.34.0.tar.gz |
| Windows binary (x86_64) | SeqSQC_1.34.0.zip |
| macOS binary (arm64) | SeqSQC_1.34.0.tgz |
| macOS binary (x86_64) | SeqSQC_1.34.0.tgz |
Dependencies
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