recipe r-dimsum

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies

Homepage:

https://github.com/lehner-lab/DiMSum

License:

MIT

Recipe:

/r-dimsum/meta.yaml

package r-dimsum

versions:

1.3.1-0,  1.3-2,  1.3-1,  1.3-0,  1.2.11-1,  1.2.11-0,  1.2.10-0,  1.2.9-0,  1.2.8-0, 

1.3.1-0,  1.3-2,  1.3-1,  1.3-0,  1.2.11-1,  1.2.11-0,  1.2.10-0,  1.2.9-0,  1.2.8-0,  1.2.7-2,  1.2.7-1,  1.2.7-0,  1.2.5-0,  1.2.0-0,  1.1.4-0,  1.1.3-0

depends bioconductor-biostrings:

depends bioconductor-iranges:

depends bioconductor-shortread:

depends cutadapt:

2.4.*

depends fastqc:

0.11.*

depends pandoc:

>=1.17.2

depends r-base:

>=4.0,<4.1.0a0

depends r-cairo:

depends r-cowplot:

depends r-data.table:

depends r-ggally:

depends r-ggplot2:

depends r-gridextra:

depends r-hexbin:

depends r-optparse:

depends r-plyr:

depends r-reshape2:

depends r-rmarkdown:

depends r-seqinr:

depends r-stringr:

depends starcode:

>=1.3

depends vsearch:

>=2.17

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 r-dimsum

and update with::

   mamba update r-dimsum

To create a new environment, run:

mamba create --name myenvname r-dimsum

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-dimsum:<tag>

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

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