Cogito

DOI: 10.18129/B9.bioc.Cogito    

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

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

Bioconductor version: Development (3.15)

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>

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

Installation

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

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

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

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 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) Cogito_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Cogito
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Cogito
Package Short Url https://bioconductor.org/packages/Cogito/
Package Downloads Report Download Stats

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