recipe bioconductor-redseq

Analysis of high-throughput sequencing data processed by restriction enzyme digestion

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-redseq/meta.yaml

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

package bioconductor-redseq

versions:

1.48.0-0,  1.46.0-0,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0, 

1.48.0-0,  1.46.0-0,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.28.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-bsgenome.celegans.ucsc.ce2:

>=1.4.0,<1.5.0

depends bioconductor-chippeakanno:

>=3.36.0,<3.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-multtest:

>=2.58.0,<2.59.0

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-redseq

and update with::

   mamba update bioconductor-redseq

To create a new environment, run:

mamba create --name myenvname bioconductor-redseq

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-redseq:<tag>

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

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