recipe bioconductor-chippeakanno

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/ChIPpeakAnno.html

License:

GPL (>= 2)

Recipe:

/bioconductor-chippeakanno/meta.yaml

Links:

biotools: chippeakanno

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.

package bioconductor-chippeakanno

Versions:

3.32.0-0,  3.28.0-0,  3.26.0-0,  3.24.1-0,  3.24.0-0,  3.22.0-0,  3.20.0-0,  3.18.2-0,  3.16.0-0, 

3.32.0-0,  3.28.0-0,  3.26.0-0,  3.24.1-0,  3.24.0-0,  3.22.0-0,  3.20.0-0,  3.18.2-0,  3.16.0-0,  3.14.2-0,  3.12.0-0,  3.10.2-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-ensembldb >=2.22.0,<2.23.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-graph >=1.76.0,<1.77.0

• bioconductor-interactionset >=1.26.0,<1.27.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-keggrest >=1.38.0,<1.39.0

• bioconductor-multtest >=2.54.0,<2.55.0

• bioconductor-rbgl >=1.74.0,<1.75.0

• bioconductor-regioner >=1.30.0,<1.31.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-dbi

• r-dplyr

• r-ggplot2

• r-matrixstats

• r-venndiagram

Required By:

• bioconductor-redseq

• bioconductor-atacseqqc

• bioconductor-vulcan

• bioconductor-descan2

• bioconductor-guideseq

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-chippeakanno

and update with:

conda update bioconductor-chippeakanno

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-chippeakanno:<tag>

(see bioconductor-chippeakanno/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-chippeakanno/README.html)