recipe bioconductor-outsplice

Comparison of Splicing Events between Tumor and Normal Samples

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-outsplice/meta.yaml

An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.

package bioconductor-outsplice

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-repitools:

>=1.48.0,<1.49.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:

>=3.18.0,<3.19.0

depends r-base:

>=4.3,<4.4.0a0

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-outsplice

and update with::

   mamba update bioconductor-outsplice

To create a new environment, run:

mamba create --name myenvname bioconductor-outsplice

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-outsplice:<tag>

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

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Link to this page

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