- recipe bioconductor-rtracklayer
R interface to genome annotation files and the UCSC genome browser
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/rtracklayer.html
- License:
Artistic-2.0 + file LICENSE
- Recipe:
- Links:
biotools: rtracklayer
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
- package bioconductor-rtracklayer¶
- versions:
1.62.0-1,1.62.0-0,1.60.0-0,1.58.0-2,1.58.0-1,1.54.0-4,1.54.0-3,1.54.0-2,1.54.0-1,1.62.0-1,1.62.0-0,1.60.0-0,1.58.0-2,1.58.0-1,1.54.0-4,1.54.0-3,1.54.0-2,1.54.0-1,1.54.0-0,1.52.0-0,1.50.0-2,1.50.0-1,1.50.0-0,1.48.0-0,1.46.0-0,1.44.2-1,1.44.2-0,1.44.0-1,1.42.1-1,1.42.1-0,1.40.6-0,1.38.3-0,1.38.0-0,1.36.6-0,1.34.2-1,1.34.1-0,1.32.2-1,1.30.1-0,1.30.0-1- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocio:
>=1.12.0,<1.13.0- depends bioconductor-biocio:
>=1.12.0,<1.13.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- 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-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-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-xvector:
>=0.42.0,<0.43.0- depends bioconductor-xvector:
>=0.42.0,<0.43.0a0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.3,<4.4.0a0- depends r-rcurl:
>=1.4-2- depends r-restfulr:
>=0.0.13- depends r-restfulr:
>=0.0.15,<0.1.0a0- depends r-xml:
>=1.98-0- 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-rtracklayer and update with:: mamba update bioconductor-rtracklayer
To create a new environment, run:
mamba create --name myenvname bioconductor-rtracklayer
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-rtracklayer:<tag> (see `bioconductor-rtracklayer/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-rtracklayer/README.html)
