recipe keggcharter

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

Homepage:

https://github.com/iquasere/KEGGCharter

Documentation:

https://github.com/iquasere/KEGGCharter/blob/master/README.md

License:

BSD / BSD-3-Clause

Recipe:

/keggcharter/meta.yaml

KEGGCharter takes as input a quantification table of proteins with corresponding KEGG IDs available and maps that information into KEGG metabolic maps using the KEGG API. Both genomic potential (from either genomics or metagenomics) and gene expression quantification (from either (meta)transcriptomics or (meta)proteomics) can be represented. Genomic information is mapped in a binary exists or not rule, for each taxon available KEGGCharter will assign a color which will be included in the boxes corresponding to functions present in that taxon. Gene expression quantification is mapped as differential expression where quantification between the several columns specified is represented as a single row heatmap for each function present in the data.

package keggcharter

versions:

1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.7.1-0,  0.7.0-0,  0.6.0-0, 

1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.7.1-0,  0.7.0-0,  0.6.0-0,  0.5.1-0,  0.5.0-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.5-0,  0.3.4-0,  0.3.3-0,  0.3.2-0,  0.3.0-0,  0.2.5-0,  0.2.4-0,  0.2.3-1,  0.2.3-0,  0.2.2-0,  0.2.1-0,  0.2.0-0,  0.1.3-0,  0.1.2-0,  0.1.1-0,  0.1.0-0,  0.0.4-0,  0.0.3-0

depends biopython:

depends lxml:

depends matplotlib-base:

depends mscorefonts:

depends openpyxl:

depends pandas:

depends poppler:

depends reportlab:

depends requests:

depends tqdm:

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 keggcharter

and update with::

   mamba update keggcharter

To create a new environment, run:

mamba create --name myenvname keggcharter

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/keggcharter:<tag>

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

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