Orange Bioinformatics documentation¶
Orange Bioinformatics is an add-on for Orange data mining software package. It extends Orange by providing functionality for some elementary tasks in bioinformatics, like gene set analysis, enrichment, and access to pathway libraries. Included are also widgets for with graphical user interface for, mainly, gene expression analytics.
Widgets¶
Scripting Reference¶
- Array Express (
arrayexpress) - Bio Mart (
biomart) - Dictyostelium discoideum databases (
dicty) - D. discoideum Mutant Phenotypes (
dicty.phenotypes) - Gene name matching (
gene) - Translation of homologs (
gene.homology) - Gene sets (
geneset) - NCBI’s Gene Expression Omnibus interface (
geo) - Gene Ontology (
go) - Gene Set Enrichment Analysis (GSEA,
gsea) - KEGG - Kyoto Encyclopedia of Genes and Genomes (
kegg) - OMIM: Online Mendelian Inheritance in Man (
omim) - OBO Ontology (
ontology) - Protein-protein interactions (
ppi) - Organism Taxonomy (
taxonomy) - Probability distributions and corrections (
utils.stats)
Installation¶
To install Bioinformatics add-on for Orange from PyPi run:
pip install Orange-Bioinformatics
To install it from source code run:
python setup.py install
To build Python egg run:
python setup.py bdist_egg
To install add-on in development mode run:
python setup.py develop