- recipe bioconductor-genomation
Summary, annotation and visualization of genomic data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/genomation.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: genomation
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
- package bioconductor-genomation¶
- versions:
1.34.0-1,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.26.0-2,1.26.0-1,1.26.0-0,1.24.0-0,1.34.0-1,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.26.0-2,1.26.0-1,1.26.0-0,1.24.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-0,1.16.0-1,1.14.0-0,1.12.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.6.0-0,1.4.2-0,1.2.2-0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-impute:
>=1.76.0,<1.77.0- depends bioconductor-impute:
>=1.76.0,<1.77.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-seqpattern:
>=1.34.0,<1.35.0- depends bioconductor-seqpattern:
>=1.34.0,<1.35.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-data.table:
- depends r-ggplot2:
- depends r-gridbase:
- depends r-matrixstats:
- depends r-plotrix:
- depends r-plyr:
- depends r-rcpp:
>=0.12.14- depends r-readr:
- depends r-reshape2:
- requirements:
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-genomation and update with:: mamba update bioconductor-genomation
To create a new environment, run:
mamba create --name myenvname bioconductor-genomation
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-genomation:<tag> (see `bioconductor-genomation/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-genomation/README.html)
