SeqSQC
A bioconductor package for sample quality check with next generation sequencing data
Bioconductor version: 3.24 · Package version: 1.35.0
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 |
| Downloads rank | 595 |
| Source branch | devel |
| biocViews | Experiment Data, Genome, Homo_sapiens_Data, Project1000genomes, Sequencing Data, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SeqSQC_1.35.0.tar.gz |
| Windows binary (x86_64) | SeqSQC_1.35.0.zip |
| macOS binary (arm64) | SeqSQC_1.35.0.tgz |
| macOS binary (x86_64) | SeqSQC_1.35.0.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