- recipe bioconductor-gviz
Plotting data and annotation information along genomic coordinates
- Homepage:
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: gviz
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
- package bioconductor-gviz¶
- versions:
1.50.0-0,1.46.1-0,1.44.0-0,1.42.0-0,1.38.0-0,1.36.1-0,1.34.1-0,1.34.0-0,1.32.0-0,1.50.0-0,1.46.1-0,1.44.0-0,1.42.0-0,1.38.0-0,1.36.1-0,1.34.1-0,1.34.0-0,1.32.0-0,1.30.0-0,1.28.0-1,1.26.4-0,1.24.0-0,1.22.3-0,1.22.0-0,1.20.0-0,1.16.5-2,1.14.2-0- depends bioconductor-annotationdbi:
>=1.68.0,<1.69.0- depends bioconductor-biobase:
>=2.66.0,<2.67.0- 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-biovizbase:
>=1.54.0,<1.55.0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0- 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-iranges:
>=2.40.0,<2.41.0- 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-xvector:
>=0.46.0,<0.47.0- depends r-base:
>=4.4,<4.5.0a0- depends r-digest:
>=0.6.8- depends r-lattice:
- depends r-latticeextra:
>=0.6-26- depends r-matrixstats:
>=0.8.14- depends r-rcolorbrewer:
- 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-gviz and update with:: mamba update bioconductor-gviz
To create a new environment, run:
mamba create --name myenvname bioconductor-gviz
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-gviz:<tag> (see `bioconductor-gviz/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-gviz/README.html)
