krishnanlab/PyGenePlexus

Issues

• convert task to more readable may break code

  #326 opened 3 months ago by ChristopherMancuso
  0

• get list of genes that is important for similairty tables

  #324 opened 3 months ago by ChristopherMancuso
  0

• allow users to specify negatives

  #321 opened 4 months ago by ChristopherMancuso
  1

• simultaneously run two species

  #323 opened 4 months ago by ChristopherMancuso
  0

• Return information on neutrals

  #237 opened 2 years ago by ChristopherMancuso
  1

• Display of genes not mapped to entrez

  #195 opened 4 months ago by ChristopherMancuso
  1

• number of file limit in Zenodo

  #318 opened 4 months ago by ChristopherMancuso
  1

• Reproducibility and Documentation

  #322 opened 4 months ago by ChristopherMancuso
  1

• change cv results for small genesets

  #314 opened 4 months ago by ChristopherMancuso
  4

• a gene name to input gene conversion table

  #316 opened 4 months ago by ChristopherMancuso
  2

• property and setter decorators broken

  #320 opened 4 months ago by ChristopherMancuso
  0

• CLI does save isolated genes

  #319 opened 4 months ago by ChristopherMancuso
  0

• add one-to-one orthologs for cross species transfer predictions

  #317 opened 4 months ago by ChristopherMancuso
  0

• a gsc description for similarities results

  #315 opened 4 months ago by ChristopherMancuso
  0

• Run on all comb of net-feat, generate summary results/plots

  #123 opened 4 months ago by RemyLau
  1

• Doctest to make sure example scripts run as expected

  #117 opened 4 months ago by RemyLau
  1

• Custom network embeddings

  #121 opened 4 months ago by RemyLau
  1

• Pretraining models on custom network

  #122 opened 4 months ago by RemyLau
  1

• Utilities for generating subgraph (color based on pos/neg/neutral)

  #107 opened 4 months ago by RemyLau
  1

• Fix way DisGeNet annotations are being added

  #277 opened a year ago by ChristopherMancuso
  1

• Release v1.0.0

  #119 opened a year ago by RemyLau
  0

• add aggregation function

  #182 opened 2 years ago by ChristopherMancuso
  0

• More memory efficient graph generation

  #180 opened 2 years ago by ChristopherMancuso
  0

• Remove predetermined options for GSC and networks

  #143 opened 2 years ago by ChristopherMancuso
  7

• Better Choose Validation Dataframe Networks

  #176 opened 2 years ago by ChristopherMancuso
  0

• Error with custom network and auto download on

  #175 opened 2 years ago by ChristopherMancuso
  0

• Improve custom file checking mechanisms

  #146 opened 3 years ago by RemyLau
  1

• Add task argument for CLI interface

  #142 opened 3 years ago by ChristopherMancuso
  4

• add direct link to read the docs

  #136 opened 3 years ago by ChristopherMancuso
  0

• Download run log dump to data folder

  #127 opened 3 years ago by RemyLau
  0

• Update api example

  #124 opened 3 years ago by RemyLau
  0

• v1 pre-release code review

  #80 opened 3 years ago by RemyLau
  0

• Main doc page overview

  #85 opened 3 years ago by RemyLau
  0

• Add feature for calculating "connectivity" score of a gene set

  #120 opened 3 years ago by ChristopherMancuso
  0

• Retry upper limit

  #113 opened 3 years ago by RemyLau
  0

• Run log

  #111 opened 3 years ago by RemyLau
  0

• Options to only do prediction (leave out similarities)

  #106 opened 3 years ago by RemyLau
  0

• Overwirte option

  #109 opened 3 years ago by RemyLau
  0

• Cross validation options

  #86 opened 3 years ago by RemyLau
  0

• Options for saving cross-validation results

  #84 opened 3 years ago by RemyLau
  0

• Validate custom network specification

  #83 opened 3 years ago by RemyLau
  0

• Dump run config to result dir

  #78 opened 3 years ago by RemyLau
  0

• Warn results overwriting

  #76 opened 3 years ago by RemyLau
  0

• Warn if data downloading might take long (>15secs)

  #81 opened 3 years ago by RemyLau
  0

• Geneplexus parameter setters (property), also allow checking for incorrect options

  #79 opened 3 years ago by RemyLau
  0

• Clean data directory

  #88 opened 3 years ago by RemyLau
  0

• GenePlexus object auto data download option

  #89 opened 3 years ago by RemyLau
  0

• Need to catch missing files

  #90 opened 3 years ago by RemyLau
  0

• Silent/quite cli option (-q, --quite)

  #77 opened 3 years ago by RemyLau
  0

• Use lowercase ``gsc``

  #82 opened 3 years ago by RemyLau
  0