seqCAT

DOI: 10.18129/B9.bioc.seqCAT    

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

High Throughput Sequencing Cell Authentication Toolkit

Bioconductor version: Development (3.8)

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 <erikfas at kth.se>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("seqCAT", version = "devel")

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 1.3.5
License MIT + file LICENCE
Depends R (>= 3.5), 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), lazyeval (>= 0.2.0), methods, 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
Links To Me
Build Report  

Package Archives

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

Source Package seqCAT_1.3.5.tar.gz
Windows Binary seqCAT_1.3.5.zip
Mac OS X 10.11 (El Capitan) seqCAT_1.3.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/seqCAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqCAT
Package Short Url http://bioconductor.org/packages/seqCAT/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: