Code

Regulatory#18

Code

Merged

ctrlaltaf merged 27 commits intomainReed-CompBio/protein-function-prediction:mainfrom regulatoryReed-CompBio/protein-function-prediction:regulatoryCopy head branch name to clipboardSep 9, 2024

+2,927,321-275,644

Commits

Commits on Jun 26, 2024

• updated difference function for more recent workflow, added a go_neighbors that returns how many go terms are annotated to each protein and in what frequency, a reverse_sample function that samples…

  Show description for 9ab178d
  

  amnorman

  committed
  9ab178d

Commits on Jun 27, 2024

• updated reverse_sample to run faster and added proteins with no annotated go terms the distribution in go_neighbors

  

  amnorman

  committed
  66095a3

Commits on Jul 8, 2024

• added random walk

  

  amnorman

  committed
  3969307

Commits on Jul 9, 2024

• new random walk and test file using small graphs

  

  amnorman

  committed
  5daac45

Commits on Jul 19, 2024

• Changed numbering of random walks and added V3 & V5 (refer to google doc for what they do), also added protein only and progo only networks.

  

  amnorman

  committed
  aacbbda

Commits on Jul 22, 2024

• test file with neighbor ranks and .csv with a list of all unique go terms

  

  amnorman

  committed
  60cbf57

• fixed merge conflict

  ctrlaltaf

  committed
  d8c3690

Commits on Aug 1, 2024

• Cleaned up files, added to README for .py files, updated pytests

  

  amnorman

  committed
  ccc00d5

• fixed pytest

  

  amnorman

  committed
  e59110f

Commits on Aug 21, 2024

• testing fly mixed networks

  ctrlaltaf

  committed
  13ae1cd

Commits on Aug 22, 2024

• added new species data

  ctrlaltaf

  committed
  c94f66d

Commits on Aug 27, 2024

• all methods work with new database

  ctrlaltaf

  committed
  71fbbe7

• working sampling method

  ctrlaltaf

  committed
  90571ad

Commits on Aug 28, 2024

• added go term sampling

  ctrlaltaf

  committed
  2bd7f6c

• cleaned up code

  ctrlaltaf

  committed
  baf918c

Commits on Aug 29, 2024

• added degree and ratio sampling method

  ctrlaltaf

  committed
  d617b81

Commits on Aug 30, 2024

• optimized sampling method

  ctrlaltaf

  committed
  5a6b4cb

Commits on Sep 5, 2024

• new methods

  ctrlaltaf

  committed
  a44a4e9

Commits on Sep 9, 2024

• testing final figures workflow

  ctrlaltaf

  committed
  f42e113

• testing final figures workflow

  ctrlaltaf

  committed
  f1e9686

• changing data structure

  ctrlaltaf

  committed
  cb5ddb8

• pipeline for one species data

  ctrlaltaf

  committed
  731266c

• pipeline for one species data

  ctrlaltaf

  committed
  b10a552

• multi species data

  ctrlaltaf

  committed
  75fbd2a

• subplot for two figures

  ctrlaltaf

  committed
  49b341c

• subplot for two figures

  ctrlaltaf

  committed
  bd65d5c

• generated multi subplot for a test case

  ctrlaltaf

  committed
  457fe84