recipe bioconductor-saturn

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-saturn/meta.yaml

satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.

package bioconductor-saturn

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-boot:

depends r-ggplot2:

depends r-locfdr:

depends r-matrix:

depends r-pbapply:

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-saturn

and update with::

   mamba update bioconductor-saturn

To create a new environment, run:

mamba create --name myenvname bioconductor-saturn

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-saturn:<tag>

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

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