biolab/orange3-bioinformatics

GO Enrichment Analysis

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#2 opened on Feb 5, 2018

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enhancementhelp wantedpriority-low

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Description

Current gene ontology enrichment runs quite slow and consumes a lot of system memory.

The proposal is, that we use gotea module from Genialis repository: https://github.com/genialis/gotea

Usage: https://github.com/genialis/resolwe-bio/blob/master/resolwe_bio/tools/goea.py#L64

This change will introduce a major redesign in current GO module and OWGOBrowser widget.

Contributor guide

Research direction
Study the gotea library from Genialis (https://github.com/genialis/gotea) and its usage in resolwe bio. Redesign the current GO module and OWGOBrowser widget to integrate gotea, replacing the existing slow implementation.
Tech stack
python
Domain
bioinformatics
Issue type
Refactor
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-2 days
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Stale
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
PythonGit
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
30