SeqSQC
This is the released version of SeqSQC; for the devel version, see SeqSQC.
A bioconductor package for sample quality check with next generation sequencing data
Bioconductor version: Release (3.23)
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("SeqSQC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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
| 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | SeqSQC_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | SeqSQC_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | SeqSQC_1.34.0.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 |