recipe bioconductor-dss

Dispersion shrinkage for sequencing data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/DSS.html

License:

GPL-3.0-only

Recipe:

/bioconductor-dss/meta.yaml

Links:

biotools: dss

DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

package bioconductor-dss

versions:

2.48.0-1,  2.48.0-0,  2.46.0-1,  2.46.0-0,  2.42.0-2,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-1, 

2.48.0-1,  2.48.0-0,  2.46.0-1,  2.46.0-0,  2.42.0-2,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-1,  2.38.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-1,  2.30.0-0,  2.28.0-0,  2.26.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-bsseq:

>=1.38.0,<1.39.0

depends bioconductor-bsseq:

>=1.38.0,<1.39.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

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-dss

and update with::

   mamba update bioconductor-dss

To create a new environment, run:

mamba create --name myenvname bioconductor-dss

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-dss:<tag>

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

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