seqCAT

This is the released version of seqCAT; for the devel version, see seqCAT.

High Throughput Sequencing Cell Authentication Toolkit

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DOI: 10.18129/B9.bioc.seqCAT

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, GenomicVariation, Sequencing, Software, VariantAnnotation

Version 1.32.0

In Bioconductor since BioC 3.6 (R-3.4) (8 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

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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_1.32.0.tar.gz

Windows Binary (x86_64) seqCAT_1.31.0.zip

macOS Binary (x86_64) seqCAT_1.32.0.tgz

macOS Binary (arm64) seqCAT_1.32.0.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/

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