seqCAT

DOI: 10.18129/B9.bioc.seqCAT  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see seqCAT.

High Throughput Sequencing Cell Authentication Toolkit

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	seqCAT: The High Throughput Sequencing Cell Authentication Toolkit
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, GenomicVariation, Sequencing, Software, VariantAnnotation
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
LinkingTo
Suggests	knitr, BiocStyle, rmarkdown, testthat, BiocManager
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	seqCAT_1.20.0.tar.gz
Windows Binary	seqCAT_1.20.0.zip (64-bit only)
macOS Binary (x86_64)	seqCAT_1.20.0.tgz
macOS Binary (arm64)	seqCAT_1.20.0.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