Cogito

DOI: 10.18129/B9.bioc.Cogito  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see Cogito.

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Bioconductor version: 3.17

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

Author: Annika Bürger [cre, aut]

Maintainer: Annika Bürger <a.buerger at uni-muenster.de>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Cogito")

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("Cogito")

 

HTML	R Script	Cogito: Compare annotated genomic intervals tool
PDF		Reference Manual
Text		NEWS

Details

biocViews	FunctionalGenomics, GeneRegulation, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	LGPL-3
Depends	R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy
Imports	BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene
LinkingTo
Suggests	BiocStyle, knitr, markdown, testthat (>= 3.0.0)
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	Cogito_1.6.0.tar.gz
Windows Binary	Cogito_1.6.0.zip
macOS Binary (x86_64)	Cogito_1.6.0.tgz
macOS Binary (arm64)	Cogito_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Cogito
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Cogito
Bioc Package Browser	https://code.bioconductor.org/browse/Cogito/
Package Short Url	https://bioconductor.org/packages/Cogito/
Package Downloads Report	Download Stats