recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/ChIPpeakAnno.html

License

GPL (>= 2)

Recipe

/bioconductor-chippeakanno/meta.yaml

Links

biotools: chippeakanno

package bioconductor-chippeakanno

(downloads) docker_bioconductor-chippeakanno

Versions

3.16.0-0, 3.14.2-0, 3.12.0-0, 3.10.2-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biomart

>=2.38.0,<2.39.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-bsgenome

>=1.50.0,<1.51.0

Depends bioconductor-delayedarray

>=0.8.0,<0.9.0

Depends bioconductor-ensembldb

>=2.6.0,<2.7.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicfeatures

>=1.34.0,<1.35.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-go.db

>=3.7.0,<3.8.0

Depends bioconductor-graph

>=1.60.0,<1.61.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-multtest

>=2.38.0,<2.39.0

Depends bioconductor-rbgl

>=1.58.0,<1.59.0

Depends bioconductor-regioner

>=1.14.0,<1.15.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-biocmanager

Depends r-dbi

Depends r-idr

Depends r-matrixstats

Depends r-seqinr

Depends r-venndiagram

Requirements

Installation

With an activated Bioconda channel (see 2. 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>)