recipe bioconductor-splicinggraphs

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SplicingGraphs.html

License:

Artistic-2.0

Recipe:

/bioconductor-splicinggraphs/meta.yaml

Links:

biotools: splicinggraphs, doi: 10.1093/bioinformatics/18.suppl_1.s181

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

package bioconductor-splicinggraphs

versions:

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.25.0-0, 

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.25.0-0,  1.24.0-1,  1.22.1-0,  1.20.0-0,  1.18.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rgraphviz:

>=2.46.0,<2.47.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-igraph:

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-splicinggraphs

and update with::

   mamba update bioconductor-splicinggraphs

To create a new environment, run:

mamba create --name myenvname bioconductor-splicinggraphs

with myenvname being 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-splicinggraphs:<tag>

(see `bioconductor-splicinggraphs/tags`_ for valid values for ``<tag>``)

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