recipe bioconductor-magpie

MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-magpie/meta.yaml

This package aims to perform power analysis for the MeRIP-seq study. It calculates FDR, FDC, power, and precision under various study design parameters, including but not limited to sample size, sequencing depth, and testing method. It can also output results into .xlsx files or produce corresponding figures of choice.

package bioconductor-magpie

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

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 bioconductor-tress:

>=1.8.0,<1.9.0

depends r-aod:

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

depends r-matrixstats:

depends r-openxlsx:

depends r-rcolorbrewer:

depends r-reshape2:

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-magpie

and update with::

   mamba update bioconductor-magpie

To create a new environment, run:

mamba create --name myenvname bioconductor-magpie

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-magpie:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-magpie/README.html)