seqCAT
This is the released version of seqCAT; for the devel version, see seqCAT.
High Throughput Sequencing Cell Authentication Toolkit
Bioconductor version: Release (3.23)
The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.
Author: Erik Fasterius [aut, cre]
Maintainer: Erik Fasterius <erik.fasterius at outlook.com>
citation("seqCAT")):
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("seqCAT")
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("seqCAT")| seqCAT: The High Throughput Sequencing Cell Authentication Toolkit | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, GenomicVariation, Sequencing, Software, VariantAnnotation |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | MIT + file LICENCE |
| Depends | R (>= 3.6), GenomicRanges(>= 1.26.4), VariantAnnotation(>= 1.20.3) |
| Imports | dplyr (>= 0.5.0), GenomeInfoDb(>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges(>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors(>= 0.12.2), stats, SummarizedExperiment(>= 1.4.0), tidyr (>= 0.6.1), utils |
| System Requirements | |
| URL |
See More
| Suggests | knitr, BiocStyle, rmarkdown, testthat, BiocManager |
| 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 | seqCAT_1.34.0.tar.gz |
| Windows Binary (x86_64) | seqCAT_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | seqCAT_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | seqCAT_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/seqCAT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/seqCAT |
| Bioc Package Browser | https://code.bioconductor.org/browse/seqCAT/ |
| Package Short Url | https://bioconductor.org/packages/seqCAT/ |
| Package Downloads Report | Download Stats |