recipe riboseqc

Read length specific QC of Ribo-seq data

Homepage:

https://github.com/ohlerlab/RiboseQC

License:

GPL3 / GPL-3

Recipe:

/riboseqc/meta.yaml

A powerful analysis tool for the analysis of Ribo-seq data, which is able to provide read-length specific analysis of both cytoplasmic and organellar ribosome, and provides interactive visualization of results in a dynamic html report

package riboseqc

versions:

1.1-1,  1.1-0

depends bioconductor-biocgenerics:

depends bioconductor-biostrings:

depends bioconductor-bsgenome:

depends bioconductor-genomicalignments:

depends bioconductor-genomicfeatures:

depends bioconductor-genomicfiles:

depends bioconductor-rtracklayer:

depends r-ade4:

depends r-base:

>=3.6,<3.7.0a0

depends r-devtools:

depends r-domc:

depends r-foreach:

depends r-ggplot2:

depends r-ggpubr:

depends r-gridextra:

depends r-iterators:

depends r-jsonlite:

depends r-knitr:

depends r-multitaper:

depends r-r.methodss3:

depends r-reshape2:

depends r-rmarkdown:

depends r-seqinr:

depends r-viridis:

depends r-xnomial:

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 riboseqc

and update with::

   mamba update riboseqc

To create a new environment, run:

mamba create --name myenvname riboseqc

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/riboseqc:<tag>

(see `riboseqc/tags`_ for valid values for ``<tag>``)

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