recipe bioconductor-rmspc

Multiple Sample Peak Calling

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-rmspc/meta.yaml

The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as "peaks"), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.

package bioconductor-rmspc

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-processx:

depends r-stringr:

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-rmspc

and update with::

   mamba update bioconductor-rmspc

To create a new environment, run:

mamba create --name myenvname bioconductor-rmspc

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-rmspc:<tag>

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

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