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 (3.20)

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 "4.4") and enter:


if (!require("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")
Cogito: Compare annotated genomic intervals tool HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FunctionalGenomics, GeneRegulation, Sequencing, Software
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
System Requirements
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Suggests BiocStyle, knitr, markdown, testthat (>= 3.0.0)
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Package Archives

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

Source Package Cogito_1.11.0.tar.gz
Windows Binary Cogito_1.11.0.zip (64-bit only)
macOS Binary (x86_64) Cogito_1.11.0.tgz
macOS Binary (arm64) Cogito_1.11.0.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