recipe r-bcalm

Barcode Analysis using linear models for MPRA data

Homepage:

https://github.com/kircherlab/BCalm

License:

MIT / MIT

Recipe:

/r-bcalm/meta.yaml

BCalm is a package that provides a modification from the mpralm package, an R package that provides tools for differential analysis in MPRA studies. BCalm allows users to use individual barcodes as model input. It provides tools for data management, count preprocessing, and differential analysis in massively parallel reporter assays (MPRA).

package r-bcalm

versions:

0.100.0-0,  0.99.0-0

depends bioconductor-biobase:

depends bioconductor-biocgenerics:

depends bioconductor-delayedarray:

depends bioconductor-genomeinfodb:

depends bioconductor-genomicranges:

depends bioconductor-iranges:

depends bioconductor-limma:

depends bioconductor-mpra:

depends bioconductor-s4vectors:

depends bioconductor-summarizedexperiment:

depends r-base:

>=4.5,<4.6.0a0

depends r-curl:

depends r-scales:

depends r-statmod:

depends r-tidyr:

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 r-bcalm

and update with::

   mamba update r-bcalm

To create a new environment, run:

mamba create --name myenvname r-bcalm

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/r-bcalm:<tag>

(see `r-bcalm/tags`_ for valid values for ``<tag>``)

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