- recipe keggcharter
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
- Homepage:
- Documentation:
https://github.com/iquasere/KEGGCharter/blob/master/README.md
- License:
BSD / BSD-3-Clause
- Recipe:
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:
on biopython
on lxml
on matplotlib-base
on mscorefonts
on openpyxl
on pandas
on poppler
on reportlab
on requests
on tqdm
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install keggcharter
to add into an existing workspace instead, run:
pixi add keggcharter
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install keggcharter
Alternatively, to install into a new environment, run:
conda create -n envname keggcharter
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/keggcharter:<tag>
(see keggcharter/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/keggcharter/README.html)
