[ENH] Add support for custom gene sets, reference genes and enrichment

[JakaKokosar]

Issue

Fixes #64
Fixes #65

Description of changes

Refactor OWGeneSets and extend this widget to support enrichment analysis.

Includes

• Code changes
• Tests
• Documentation

[codecov-io]

Codecov Report

Merging #67 into master will increase coverage by 0.29%.
The diff coverage is 37.83%.

@@            Coverage Diff             @@
##           master      #67      +/-   ##
==========================================
+ Coverage   23.43%   23.73%   +0.29%     
==========================================
  Files          37       37              
  Lines        3303     3333      +30     
==========================================
+ Hits          774      791      +17     
- Misses       2529     2542      +13

Impacted Files	Coverage Δ
orangecontrib/bioinformatics/geneset/__init__.py	41.66% <33.33%> (ø)	⬆️
orangecontrib/bioinformatics/geneset/utils.py	78.76% <38.23%> (-17.63%)	⬇️
orangecontrib/bioinformatics/utils/statistics.py	37.14% <0%> (+5.71%)	⬆️

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[BlazZupan]

I am getting a strange list of categories when using the data from Dictyostelium (see the image, and entries 5', 5, 3, and "contractile ring contraction" under GO).

[BlazZupan]

The minimum count filter can go together with the other two filter fields. Put it first, before p-value, and call it "Count". The default is checked, with a minimal count set to 5.

Some minor corrections:

• Maximum False discovery rate -> Maximum false discovery rate (in mouse-over text)
• Maximum p-value -> Maximum p-value of the enrichment score (in mouse-over text)
• Gene Set Databases - > Gene Set Categories
• In the hierarchy under Gene Sets Databases, remove the table header "Category"

[BlazZupan]

This widget can be called Gene Set Enrichment. It can replace Gene Sets widget (remove the widget, but use its icon). The current icon for Set Enrichment is an old one and can be removed.