recipe bioconductor-bandits

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-bandits/meta.yaml

BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.

package bioconductor-bandits

versions:

1.18.1-0,  1.16.1-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-1, 

1.18.1-0,  1.16.1-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-drimseq:

>=1.30.0,<1.31.0

depends bioconductor-drimseq:

>=1.30.0,<1.31.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-doparallel:

depends r-dorng:

depends r-foreach:

depends r-ggplot2:

depends r-mass:

depends r-r.utils:

depends r-rcpp:

depends r-rcpparmadillo:

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-bandits

and update with::

   mamba update bioconductor-bandits

To create a new environment, run:

mamba create --name myenvname bioconductor-bandits

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-bandits:<tag>

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

Download stats

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