- 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:
- 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
- Required By:
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:
[](http://bioconda.github.io/recipes/bioconductor-chippeakanno/README.html)