Ecosyste.ms: Issues

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GitHub / fraenkel-lab/OmicsIntegrator2 issues and pull requests

#117 - Bump scikit-learn from 1.4 to 1.5.0

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#116 - update python

Pull Request - State: closed - Opened by alexlenail 10 months ago

#115 - update python

Pull Request - State: closed - Opened by alexlenail 10 months ago

#114 - Recommended citation

Issue - State: open - Opened by agitter over 2 years ago - 1 comment

#112 - Document parameter gamma (self.params.g) in the code, and re-generate docs

Issue - State: open - Opened by alexlenail over 3 years ago - 1 comment

#111 - Numeric arguments in `__main__.py` stored as list

Issue - State: open - Opened by agitter over 3 years ago

#110 - TypeError: pcst_fast(): incompatible function arguments

Issue - State: open - Opened by agitter over 3 years ago - 8 comments

#109 - Resolve package dependencies for installation

Pull Request - State: open - Opened by agitter over 3 years ago - 2 comments

#108 - Initialization parameters not used in grid search

Issue - State: open - Opened by iamjli almost 4 years ago

#107 - Is there any way to run this without a dependency on pcst_fast?

Issue - State: closed - Opened by sgosline over 4 years ago - 4 comments

#106 - KeyError when running from Jupyter

Issue - State: closed - Opened by robd02130 about 5 years ago - 1 comment

#105 - Updated setting of node attributes to work with write_graphml

Pull Request - State: closed - Opened by iamjli over 5 years ago - 1 comment

#104 - write graphml is buggy

Issue - State: closed - Opened by iamjli over 5 years ago - 2 comments

#103 - Parameter selection

Pull Request - State: closed - Opened by iamjli over 5 years ago - 1 comment

#102 - Add OI2_pipeline_data for example notebook

Pull Request - State: closed - Opened by iamjli over 5 years ago

#101 - Fix doc for input files and disable missing value parsing

Pull Request - State: closed - Opened by clemenshug over 5 years ago

#100 - OI2_pipeline_data directory missing

Issue - State: closed - Opened by bblum9 over 5 years ago - 1 comment

#99 - Implemented unrooted PSCF

Pull Request - State: open - Opened by iamjli over 5 years ago

#98 - Improve runtime of PCSF by unrooting PCST

Issue - State: open - Opened by iamjli almost 6 years ago - 7 comments
Labels: difficulty: intermediate

#97 - Update OI2_pipeline.ipynb

Pull Request - State: closed - Opened by iamjli almost 6 years ago

#96 - fix graphml output to allow posixpath

Pull Request - State: closed - Opened by iamjli almost 6 years ago

#95 - Move OI2 to depend on Axial for interactive graph plot

Pull Request - State: closed - Opened by alexlenail about 6 years ago - 1 comment

#94 - Small updates to get OI2_pipeline notebook running properly.

Pull Request - State: closed - Opened by iamjli about 6 years ago - 3 comments

#93 - Allow for later versions of pandas in setup.py

Issue - State: closed - Opened by alexlenail over 6 years ago - 1 comment

#92 - Randomizations: OverflowError: int too large to convert to float

Issue - State: closed - Opened by matthewfallan over 6 years ago - 5 comments

#91 - Add PCNet to available OI2 Interactomes.

Pull Request - State: closed - Opened by alexlenail over 6 years ago

#90 - OmicsIntegrator 2.2 (4/4) Docs, Changelog, Release!

Pull Request - State: closed - Opened by alexlenail over 6 years ago

#89 - Make it possible to root PCSF at a particular node

Issue - State: open - Opened by alexlenail over 6 years ago
Labels: difficulty: easy

#88 - Move to python3.6 f-strings consistently across codebase

Issue - State: open - Opened by alexlenail over 6 years ago - 1 comment
Labels: difficulty: easy

#87 - Finish tests for OmicsIntegrator "Results" methods

Issue - State: open - Opened by alexlenail over 6 years ago
Labels: difficulty: intermediate

#86 - OmicsIntegrator 2.2 (3/4): Visualization improvements

Pull Request - State: closed - Opened by alexlenail over 6 years ago - 1 comment

#85 - OmicsIntegrator 2.2 (2/4) -- full annotations

Pull Request - State: closed - Opened by alexlenail over 6 years ago

#84 - augment_with_molecular_function_terms

Issue - State: closed - Opened by alexlenail over 6 years ago
Labels: difficulty: intermediate

#83 - augment_with_biological_process_terms

Issue - State: closed - Opened by alexlenail over 6 years ago
Labels: difficulty: hard

#82 - rewrite output_networkx_graph_as_interactive_html

Issue - State: closed - Opened by alexlenail over 6 years ago
Labels: difficulty: intermediate

#81 - Incorrect output filename

Issue - State: closed - Opened by iamjli over 6 years ago - 1 comment

#80 - NetworkXError: GraphML writer does not support <class 'list'> as data values.

Issue - State: closed - Opened by iamjli over 6 years ago - 2 comments

#79 - Re-run subcellular localization notebook for kicks (again)

Pull Request - State: closed - Opened by alexlenail over 6 years ago

#78 - re-run subcellular notebook for kicks

Pull Request - State: closed - Opened by alexlenail over 6 years ago

#77 - Updated Subcellular localization annotation

Pull Request - State: closed - Opened by alexlenail over 6 years ago - 3 comments

#76 - Proposal: Remove old visualization technique

Pull Request - State: closed - Opened by alexlenail over 6 years ago - 1 comment

#75 - OmicsIntegrator 2.2 (1/4) -- Fixes & Tests

Pull Request - State: closed - Opened by alexlenail over 6 years ago - 6 comments

#74 - Add feature to remove edges between the 1-hop neighbors of a protein of interest

Issue - State: closed - Opened by alexlenail over 6 years ago - 1 comment
Labels: difficulty: intermediate

#72 - Grid randomizations

Pull Request - State: closed - Opened by iamjli over 6 years ago - 7 comments

#71 - Small fix for Issue #69 -- Update louvain package for compatibility with Networkx 2.0

Pull Request - State: closed - Opened by iamjli over 6 years ago - 3 comments

#70 - Subcellular localization -- "no location" should be referred to as NaN

Issue - State: closed - Opened by iamjli over 6 years ago - 2 comments
Labels: difficulty: easy

#69 - Louvain clustering output

Issue - State: closed - Opened by iamjli over 6 years ago - 4 comments

#68 - Update Subcellular location annotation and scripts

Pull Request - State: closed - Opened by alexlenail over 6 years ago - 2 comments

#66 - Multi PCSF

Pull Request - State: closed - Opened by AmandaKedaigle over 6 years ago

#65 - Bug fixes

Pull Request - State: closed - Opened by AmandaKedaigle over 6 years ago - 1 comment

#64 - Bug with __main__.py

Issue - State: closed - Opened by brycehwang almost 7 years ago

#63 - Update subcellular location database (bryce)

Pull Request - State: closed - Opened by alexlenail almost 7 years ago - 2 comments

#62 - Add GSLR to OI2

Pull Request - State: closed - Opened by alexlenail almost 7 years ago - 1 comment

#61 - Groups visualization

Pull Request - State: closed - Opened by alexlenail almost 7 years ago

#60 - Subcellular Localization

Pull Request - State: closed - Opened by alexlenail almost 7 years ago - 1 comment

#59 - Clean Up

Pull Request - State: closed - Opened by alexlenail about 7 years ago

#58 - New visualization

Pull Request - State: closed - Opened by alexlenail about 7 years ago

#57 - Scaling for parameters

Issue - State: closed - Opened by brycehwang about 7 years ago - 1 comment

#56 - Ernest: Avoid parameter selection by randomize & merge

Issue - State: open - Opened by alexlenail about 7 years ago
Labels: difficulty: hard

#55 - Ernest: Ranking subnetworks

Issue - State: open - Opened by alexlenail about 7 years ago
Labels: difficulty: intermediate

#54 - Ernest: randomizations heatmap should show node degree information

Issue - State: closed - Opened by alexlenail about 7 years ago - 1 comment
Labels: difficulty: intermediate

#53 - Error during randomizations

Issue - State: closed - Opened by natashapm about 7 years ago - 6 comments

#52 - Network summarization

Issue - State: closed - Opened by iamjli about 7 years ago - 6 comments
Labels: difficulty: intermediate

#51 - OI web app

Issue - State: closed - Opened by iamjli about 7 years ago - 7 comments

#50 - replace main with parameter_sweep

Pull Request - State: closed - Opened by iamjli about 7 years ago - 2 comments

#49 - Parameter search x randomizations

Pull Request - State: closed - Opened by iamjli about 7 years ago - 2 comments

#48 - Update to networkx 2.0

Issue - State: closed - Opened by alexlenail about 7 years ago - 1 comment
Labels: difficulty: easy

#47 - [WIP] Enrichment post-processing

Pull Request - State: closed - Opened by alexlenail over 7 years ago - 6 comments

#46 - Change alpha to gamma

Pull Request - State: closed - Opened by alexlenail over 7 years ago - 1 comment

#45 - Can we name alpha something else?

Issue - State: closed - Opened by AmandaKedaigle over 7 years ago - 3 comments
Labels: difficulty: easy

#44 - Web tool not working

Issue - State: closed - Opened by iamjli over 7 years ago - 2 comments

#43 - Add ability to penalize or remove nodes

Issue - State: closed - Opened by alexlenail over 7 years ago - 1 comment
Labels: difficulty: intermediate

#42 - [WIP] Move from terminal attributes to node attributes.

Pull Request - State: closed - Opened by iamjli over 7 years ago - 7 comments

#41 - Change to attribute scheme

Pull Request - State: closed - Opened by alexlenail over 7 years ago - 1 comment

#40 - Grid Search Updates

Pull Request - State: closed - Opened by alexlenail over 7 years ago - 1 comment

#39 - Edge data representation

Issue - State: closed - Opened by iamjli over 7 years ago - 4 comments
Labels: Needs More Thought

#38 - Variable attributes discussion

Issue - State: closed - Opened by iamjli over 7 years ago - 1 comment

#37 - Merge Prize Files

Pull Request - State: closed - Opened by alexlenail over 7 years ago

#36 - Write docstrings for clustering techniques

Issue - State: closed - Opened by alexlenail over 7 years ago - 7 comments
Labels: difficulty: easy

#35 - Adding negative prizes for very low mRNA expression

Issue - State: closed - Opened by alexlenail over 7 years ago - 10 comments
Labels: difficulty: intermediate

#34 - create style code for visualization

Issue - State: closed - Opened by alexlenail over 7 years ago

#33 - Add mRNA nodes & interactions to forest

Issue - State: open - Opened by AmandaKedaigle over 7 years ago - 5 comments
Labels: difficulty: intermediate

#32 - Replace "terminal attributes" scheme with "node attributes" scheme

Pull Request - State: closed - Opened by iamjli over 7 years ago - 1 comment

#31 - visualization

Pull Request - State: closed - Opened by AmandaKedaigle over 7 years ago - 3 comments

#30 - Clustering methods

Pull Request - State: closed - Opened by alexlenail over 7 years ago - 2 comments

#29 - Web-tool suggestions

Issue - State: closed - Opened by iamjli over 7 years ago - 11 comments
Labels: difficulty: hard

#28 - rewrite _random_terminals

Issue - State: closed - Opened by alexlenail over 7 years ago - 1 comment
Labels: difficulty: intermediate

#27 - Wrapper scripts TODO list

Issue - State: closed - Opened by iamjli over 7 years ago - 4 comments

#26 - Terminals not in results included in final network

Issue - State: closed - Opened by AmandaKedaigle over 7 years ago - 3 comments

#25 - small fixes

Pull Request - State: closed - Opened by iamjli over 7 years ago

#23 - running on local machine

Issue - State: closed - Opened by iamjli over 7 years ago - 6 comments

#22 - Grid Search over parameter space

Issue - State: closed - Opened by alexlenail over 7 years ago

#21 - exclude_terminals

Issue - State: closed - Opened by alexlenail over 7 years ago - 2 comments
Labels: difficulty: intermediate

#20 - Grid Search, and other improvements

Pull Request - State: closed - Opened by alexlenail over 7 years ago

#19 - Refactor randomizations and output_forest_as_networkx

Issue - State: closed - Opened by alexlenail over 7 years ago

#17 - Write informative README

Issue - State: closed - Opened by alexlenail over 7 years ago - 3 comments

#12 - Post Processing: Clustering and Enriching

Issue - State: closed - Opened by divyaramamoorthy over 7 years ago - 18 comments