Cogito
This package is for version 3.16 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: 3.16
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("Cogito")):
Installation
To install this package, start R (version "4.2") 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")| Cogito: Compare annotated genomic intervals tool | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, GeneRegulation, Sequencing, Software |
| Version | 1.4.0 |
| 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 | |
| URL |
See More
| Suggests | BiocStyle, knitr, markdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Cogito_1.4.0.tar.gz |
| Windows Binary | Cogito_1.4.0.zip |
| macOS Binary (x86_64) | Cogito_1.4.0.tgz |
| macOS Binary (arm64) | Cogito_1.4.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |