- recipe bioconductor-girafe
Genome Intervals and Read Alignments for Functional Exploration
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/girafe.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: girafe
The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.
- package bioconductor-girafe¶
- versions:
1.54.0-1,1.54.0-0,1.52.0-0,1.50.0-1,1.50.0-0,1.46.0-2,1.46.0-1,1.46.0-0,1.44.0-0,1.54.0-1,1.54.0-0,1.52.0-0,1.50.0-1,1.50.0-0,1.46.0-2,1.46.0-1,1.46.0-0,1.44.0-0,1.42.0-1,1.42.0-0,1.40.0-0,1.38.0-0,1.36.0-1,1.34.0-0,1.32.0-0,1.30.0-0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-genomeintervals:
>=1.58.0,<1.59.0- depends bioconductor-genomeintervals:
>=1.58.0,<1.59.0a0- 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-shortread:
>=1.60.0,<1.61.0- depends bioconductor-shortread:
>=1.60.0,<1.61.0a0- 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-intervals:
>=0.13.1- 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-girafe and update with:: mamba update bioconductor-girafe
To create a new environment, run:
mamba create --name myenvname bioconductor-girafe
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-girafe:<tag> (see `bioconductor-girafe/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-girafe/README.html)
