- recipe bioconductor-vasp
Quantification and Visualization of Variations of Splicing in Population
- Homepage:
- License:
GPL (>= 2.0)
- Recipe:
Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)
- package bioconductor-vasp¶
- versions:
1.14.0-0
,1.12.0-0
,1.10.0-0
,1.6.0-0
,1.4.0-0
,1.2.4-0
,1.2.0-0
,1.0.0-0
- depends bioconductor-ballgown:
>=2.34.0,<2.35.0
- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0
- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0
- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0
- depends bioconductor-iranges:
>=2.36.0,<2.37.0
- 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-cluster:
- depends r-matrixstats:
- 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-vasp and update with:: mamba update bioconductor-vasp
To create a new environment, run:
mamba create --name myenvname bioconductor-vasp
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-vasp:<tag> (see `bioconductor-vasp/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-vasp/README.html)