- recipe bioconductor-chippeakanno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/ChIPpeakAnno.html
- License:
GPL (>= 2)
- Recipe:
- Links:
biotools: chippeakanno
The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.
- package bioconductor-chippeakanno¶
- versions:
3.40.0-0,3.36.0-0,3.34.1-0,3.32.0-0,3.28.0-0,3.26.0-0,3.24.1-0,3.24.0-0,3.22.0-0,3.40.0-0,3.36.0-0,3.34.1-0,3.32.0-0,3.28.0-0,3.26.0-0,3.24.1-0,3.24.0-0,3.22.0-0,3.20.0-0,3.18.2-0,3.16.0-0,3.14.2-0,3.12.0-0,3.10.2-0- depends bioconductor-annotationdbi:
>=1.68.0,<1.69.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biomart:
>=2.62.0,<2.63.0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0- depends bioconductor-ensembldb:
>=2.30.0,<2.31.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomicalignments:
>=1.42.0,<1.43.0- depends bioconductor-genomicfeatures:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-graph:
>=1.84.0,<1.85.0- depends bioconductor-interactionset:
>=1.34.0,<1.35.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-keggrest:
>=1.46.0,<1.47.0- depends bioconductor-multtest:
>=2.62.0,<2.63.0- depends bioconductor-pwalign:
>=1.2.0,<1.3.0- depends bioconductor-rbgl:
>=1.82.0,<1.83.0- depends bioconductor-regioner:
>=1.38.0,<1.39.0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends bioconductor-universalmotif:
>=1.24.0,<1.25.0- depends r-base:
>=4.4,<4.5.0a0- depends r-data.table:
- depends r-dbi:
- depends r-dplyr:
- depends r-ggplot2:
- depends r-matrixstats:
- depends r-scales:
- depends r-stringr:
- depends r-tibble:
- depends r-tidyr:
- depends r-venndiagram:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-chippeakanno and update with:: mamba update bioconductor-chippeakanno
To create a new environment, run:
mamba create --name myenvname bioconductor-chippeakanno
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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)
