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Bioconductor - seqCAT (development version)

seqCAT

This is the development version of seqCAT; for the stable release version, see seqCAT.

High Throughput Sequencing Cell Authentication Toolkit

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.31.0 In Bioconductor since BioC 3.6 (R-3.4) (7.5 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 System Requirements URL See More Package Archives

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

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