recipe bioconductor-oveseg

OVESEG-test to detect tissue/cell-specific markers

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-oveseg/meta.yaml

An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.

package bioconductor-oveseg

versions:

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.0-2,  1.10.0-1,  1.10.0-0,  1.8.0-0, 

1.22.0-0,  1.18.0-0,  1.16.0-0,  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:

>=1.40.0,<1.41.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0a0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-limma:

>=3.62.0,<3.63.0a0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libcxx:

>=18

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

depends r-fdrtool:

depends r-rcpp:

requirements:

additional platforms:

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-oveseg

and update with::

   mamba update bioconductor-oveseg

To create a new environment, run:

mamba create --name myenvname bioconductor-oveseg

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-oveseg:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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