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seqCAT

High Throughput Sequencing Cell Authentication Toolkit


Bioconductor version: Release (3.18)

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 (from within R, enter citation("seqCAT")):

Installation

To install this package, start R (version "4.3") 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 PDF
NEWS Text

Details

biocViews Coverage, GenomicVariation, Sequencing, Software, VariantAnnotation
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
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Suggests knitr, BiocStyle, rmarkdown, testthat, BiocManager
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package seqCAT_1.24.0.tar.gz
Windows Binary seqCAT_1.24.0.zip
macOS Binary (x86_64) seqCAT_1.24.0.tgz
macOS Binary (arm64) seqCAT_1.24.0.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