recipe bioconductor-seqgate

Filtering of Lowly Expressed Features

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/SeqGate.html

License:

GPL (>= 2.0)

Recipe:

/bioconductor-seqgate/meta.yaml

Filtering of lowly expressed features (e.g. genes) is a common step before performing statistical analysis, but an arbitrary threshold is generally chosen. SeqGate implements a method that rationalize this step by the analysis of the distibution of counts in replicate samples. The gate is the threshold above which sequenced features can be considered as confidently quantified.

package bioconductor-seqgate

versions:

1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.1-0,  1.0.0-0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-biocmanager:

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-seqgate

and update with::

   mamba update bioconductor-seqgate

To create a new environment, run:

mamba create --name myenvname bioconductor-seqgate

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-seqgate:<tag>

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

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