fraenkel-lab/OmicsIntegrator2

Issues

• Recommended citation

  #114 opened 2 years ago by agitter
  1

• Move to python3.6 f-strings consistently across codebase

  #88 opened 6 years ago by alexlenail
  1

• Is there any way to run this without a dependency on pcst_fast?

  #107 opened 5 years ago by sgosline
  4

• Node names missing in dataframe from `get_networkx_graph_as_dataframe_of_edges`

  #113 opened 4 years ago by agitter
  0

• TypeError: pcst_fast(): incompatible function arguments

  #110 opened 4 years ago by agitter
  8

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

  #112 opened 4 years ago by alexlenail
  1

• Numeric arguments in `__main__.py` stored as list

  #111 opened 4 years ago by agitter
  0

• Network summarization

  #52 opened 4 years ago by iamjli
  6

• OI2_pipeline_data directory missing

  #100 opened 4 years ago by bblum9
  1

• KeyError when running from Jupyter

  #106 opened 4 years ago by robd02130
  1

• Initialization parameters not used in grid search

  #108 opened 4 years ago by iamjli
  0

• write graphml is buggy

  #104 opened 5 years ago by iamjli
  2

• Improve runtime of PCSF by unrooting PCST

  #98 opened 6 years ago by iamjli
  7

• Allow for later versions of pandas in setup.py

  #93 opened 6 years ago by alexlenail
  1

• Randomizations: OverflowError: int too large to convert to float

  #92 opened 6 years ago by matthewfallan
  5

• rewrite output_networkx_graph_as_interactive_html

  #82 opened 6 years ago by alexlenail
  0

• Make it possible to root PCSF at a particular node

  #89 opened 6 years ago by alexlenail
  0

• Finish tests for OmicsIntegrator "Results" methods

  #87 opened 6 years ago by alexlenail
  0

• augment_with_molecular_function_terms

  #84 opened 6 years ago by alexlenail
  0

• augment_with_biological_process_terms

  #83 opened 6 years ago by alexlenail
  0

• Ernest: Ranking subnetworks

  #55 opened 7 years ago by alexlenail
  0

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

  #74 opened 6 years ago by alexlenail
  1

• Switch all soon-to-be-deprecated .loc's to .reindex's in graph.py

  #73 opened 6 years ago by alexlenail
  0

• Ernest: randomizations heatmap should show node degree information

  #54 opened 6 years ago by alexlenail
  1

• Adding negative prizes for very low mRNA expression

  #35 opened 6 years ago by alexlenail
  10

• Scaling for parameters

  #57 opened 6 years ago by brycehwang
  1

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

  #70 opened 6 years ago by iamjli
  2

• rewrite _random_terminals

  #28 opened 6 years ago by alexlenail
  1

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

  #80 opened 6 years ago by iamjli
  2

• Incorrect output filename

  #81 opened 6 years ago by iamjli
  1

• Louvain clustering output

  #69 opened 7 years ago by iamjli
  4

• Bug with __main__.py

  #64 opened 7 years ago by brycehwang
  0

• Error during randomizations

  #53 opened 7 years ago by natashapm
  6

• Update to networkx 2.0

  #48 opened 7 years ago by alexlenail
  1

• OI web app

  #51 opened 7 years ago by iamjli
  7

• Ernest: Avoid parameter selection by randomize & merge

  #56 opened 7 years ago by alexlenail
  0

• Edge data representation

  #39 opened 7 years ago by iamjli
  4

• Can we name alpha something else?

  #45 opened 7 years ago by AmandaKedaigle
  3

• Web-tool suggestions

  #29 opened 7 years ago by iamjli
  11

• Write docstrings for clustering techniques

  #36 opened 7 years ago by alexlenail
  7

• Web tool not working

  #44 opened 7 years ago by iamjli
  2

• Add ability to penalize or remove nodes

  #43 opened 7 years ago by alexlenail
  1

• Variable attributes discussion

  #38 opened 7 years ago by iamjli
  1

• Add mRNA nodes & interactions to forest

  #33 opened 7 years ago by AmandaKedaigle
  5

• Wrapper scripts TODO list

  #27 opened 7 years ago by iamjli
  4

• create style code for visualization

  #34 opened 7 years ago by alexlenail
  0

• Grid Search over parameter space

  #22 opened 7 years ago by alexlenail
  0

• Terminals not in results included in final network

  #26 opened 8 years ago by AmandaKedaigle
  3

• running on local machine

  #23 opened 8 years ago by iamjli
  6

• Seg fault

  #24 opened 8 years ago by iamjli
  7