recipe bioconductor-rnamodr

Detection of post-transcriptional modifications in high throughput sequencing data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-rnamodr/meta.yaml

RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.

package bioconductor-rnamodr

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.2-0,  1.4.0-0,  1.2.1-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-modstrings:

>=1.18.0,<1.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-colorramps:

depends r-ggplot2:

depends r-matrixstats:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rocr:

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-rnamodr

and update with::

   mamba update bioconductor-rnamodr

To create a new environment, run:

mamba create --name myenvname bioconductor-rnamodr

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-rnamodr:<tag>

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

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