recipe bioconductor-r3cseq

Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/r3Cseq.html

License:

GPL-3

Recipe:

/bioconductor-r3cseq/meta.yaml

Links:

biotools: r3cseq, doi: 10.1093/nar/gkt373

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.

package bioconductor-r3cseq

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,  1.26.0-0,  1.24.0-0,  1.22.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-rcolorbrewer:

depends r-sqldf:

depends r-vgam:

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-r3cseq

and update with::

   mamba update bioconductor-r3cseq

To create a new environment, run:

mamba create --name myenvname bioconductor-r3cseq

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-r3cseq:<tag>

(see `bioconductor-r3cseq/tags`_ for valid values for ``<tag>``)

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