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Marko Toplak committed 0da6d85

Add forgotten documentation files.

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docs/rst/reference/gene.homology.rst

+============================================================
+Translation of homologs (:mod:`gene.homology`)
+============================================================
+
+.. py:currentmodule:: Orange.bio.gene.homology
+
+This module is an interface to `NCBI HomoloGene <http://www.ncbi.nlm.nih.gov/homologene/>`_.
+
+.. autofunction::  Orange.bio.gene.homology.all_genes
+
+.. autofunction::  Orange.bio.gene.homology.homologs
+
+.. autofunction::  Orange.bio.gene.homology.homolog
+
+.. autofunction::  Orange.bio.gene.homology.orthologs
+
+.. autofunction::  Orange.bio.gene.homology.all_genes_inParanoid
+
+Examples
+--------
+
+Mapping homologs from yeast to human:
+
+.. literalinclude:: code/homology-yeast-to-human.py
+

docs/rst/reference/taxonomy.rst

+============================================================
+Organism Taxonomy (:mod:`taxonomy`)
+============================================================
+
+.. py:currentmodule:: Orange.bio.taxonomy
+
+This module provides access to the `NCBI's organism taxonomy information <http://www.ncbi.nlm.nih.gov/Taxonomy/>`_ and organism name unification across different modules. The taxonomy information is pre-loaded, that is, becomes available with installation. The list of names of the organisms are also updated with information from :obj:`Orange.bio.kegg` and :obj:`Orange.bio.go`, so that you can use organism aliases from these databases.
+
+.. autofunction:: Orange.bio.taxonomy.name
+
+.. autofunction:: Orange.bio.taxonomy.other_names
+
+.. autofunction:: Orange.bio.taxonomy.search
+
+.. autofunction:: Orange.bio.taxonomy.lineage
+   
+.. autofunction:: Orange.bio.taxonomy.to_taxid
+
+.. autofunction:: Orange.bio.taxonomy.taxids
+
+.. autofunction:: Orange.bio.taxonomy.common_taxids
+
+.. autofunction:: Orange.bio.taxonomy.essential_taxids
+
+Examples
+--------
+
+The following script takes the list of taxonomy IDs and prints out their name:
+
+.. literalinclude:: code/taxonomy1.py
+
+The output of the script is::
+
+    3702   Arabidopsis thaliana
+    9913   Bos taurus
+    6239   Caenorhabditis elegans
+    3055   Chlamydomonas reinhardtii
+    7955   Danio rerio
+    352472 Dictyostelium discoideum AX4
+    7227   Drosophila melanogaster
+    562    Escherichia coli
+    11103  Hepatitis C virus
+    9606   Homo sapiens
+    10090  Mus musculus
+    2104   Mycoplasma pneumoniae
+    4530   Oryza sativa
+    5833   Plasmodium falciparum
+    4754   Pneumocystis carinii
+    10116  Rattus norvegicus
+    4932   Saccharomyces cerevisiae
+    4896   Schizosaccharomyces pombe
+    31033  Takifugu rubripes
+    8355   Xenopus laevis
+    4577   Zea mays
+
+