Commits · master · ibmc-meg / evoppi-predicted-interactomes

Jul 15, 2024
- Changes to Ensembl for Danio rerio · ed418675
  Hugo López-Fernández authored Jul 15, 2024
  
  ed418675
Jun 25, 2024
- Improves logging messages · d21abef8
  Hugo López-Fernández authored Jun 25, 2024
  
  d21abef8
- Changes to Ensembl for Mus musculus · 04a0e614
  Hugo López-Fernández authored Jun 25, 2024
  
  04a0e614
Jun 24, 2024
- Separates reports by target species · a5ade944
  Hugo López-Fernández authored Jun 24, 2024
  
  a5ade944
- Changes to OpenTargets · 73b4a034
  Hugo López-Fernández authored Jun 24, 2024
  
  73b4a034
Jun 05, 2024
- Disables forcing remote mode when mapping Ensembl orthologs · f8052d82
  Hugo López-Fernández authored Jun 05, 2024
  
  f8052d82
Oct 28, 2022
- Separates source and target species and adds progress information · f457e612
  Hugo López-Fernández authored Oct 28, 2022
  
  f457e612
Oct 18, 2022
- Allows setting the base directory for the caches and adds a very simple README · c9fc0c3d
  Hugo López-Fernández authored Oct 18, 2022
  
  c9fc0c3d
Oct 17, 2022
- Adds orthologs database name to the reports directory to avoid overwriting DIOPT/Ensembl files · a56939f7
  Hugo López-Fernández authored Oct 17, 2022
  
  a56939f7
- Uses new orthologs-finder environment variable · 5a9461a0
  Hugo López-Fernández authored Oct 17, 2022
  
  5a9461a0
- Adds --force parameter · cd3c7de8
  Hugo López-Fernández authored Oct 17, 2022
  
  cd3c7de8
Oct 12, 2022
- Adds orthologs database name to the reports directory to avoid overwriting DIOPT/Ensembl files · 46149e79
  Hugo López-Fernández authored Oct 12, 2022
  
  46149e79
- Adds support for Danio_rerio · b634ed7c
  Hugo López-Fernández authored Oct 12, 2022
  
  b634ed7c
- Creates DIOPT and Ensembl predicted interactomes for all model files in the same directory · 45a146e9
  Hugo López-Fernández authored Oct 12, 2022
  
  45a146e9
Oct 11, 2022

Adapts scripts to file names without PMIDs · 6bb3b557
Hugo López-Fernández authored Oct 11, 2022

6bb3b557

Improves scripts and uses remote mapping mode · f3173b42

Hugo López-Fernández authored Oct 11, 2022

Improves the main scripts (create-predicted-*.sh) so that they can be executed from
external directories. Also, uses the --only-remote-mode when using the EvoPPI
interactomes parser JAR to map gene identifiers.

f3173b42

Oct 09, 2022
- Adds tests for the creation of predicted interactomes from models · 92885c41
  Hugo López-Fernández authored Oct 09, 2022
  
  92885c41
- Fixes a bug when mapping the interactome · f2cad43a
  Hugo López-Fernández authored Oct 09, 2022
  
  f2cad43a
Oct 07, 2022
- Adds script to create predicted interactomes for patient/mutant data from Ensembl · 1c9e6299
  Hugo López-Fernández authored Oct 07, 2022
  
  1c9e6299
- Adds cleanup · 9153b5ad
  Hugo López-Fernández authored Oct 07, 2022
  
  9153b5ad
- Refactors the script to create predicted interactomes from patient/mutant predictomes using DIOPT · 3a394310
  Hugo López-Fernández authored Oct 07, 2022
  
  3a394310
- Minor fixes · ec63d357
  Hugo López-Fernández authored Oct 07, 2022
  
  ec63d357
- Adds predicted interactome creation tests · d77f05cd
  Hugo López-Fernández authored Oct 07, 2022
  
  d77f05cd
Oct 06, 2022
- Refactors DIOPT script · 8015e86d
  Hugo López-Fernández authored Oct 06, 2022
  
  8015e86d
- Refactors Ensembl script to have a set of reutilizable functions · f7d5b3e1
  Hugo López-Fernández authored Oct 06, 2022
  
  f7d5b3e1
- Fixes cache of unmapped IDs in Ensembl · af78f1ae
  Hugo López-Fernández authored Oct 06, 2022
  
  af78f1ae
Oct 05, 2022
- Skips creation of existing target files · 10383138
  Hugo López-Fernández authored Oct 05, 2022
  
  10383138
Oct 04, 2022
- Adds initial versions of Ensembl predictome creation scripts · c01bf4fb
  Hugo López-Fernández authored Oct 04, 2022
  
  c01bf4fb
- Creates all DIOPT predicted interactomes and skips existing target files · b2af1935
  Hugo López-Fernández authored Oct 04, 2022
  
  b2af1935
- Adds cache of unmapped IDs to avoid querying them repeatedly · 75cca81a
  Hugo López-Fernández authored Oct 04, 2022
  
  75cca81a
Oct 03, 2022
- Adds new scripts to create predicted interactomes for patient/mutant interactomes · 0fa391ce
  Hugo López-Fernández authored Oct 03, 2022
  
  0fa391ce
Sep 28, 2022
- Allow setting the columns to map · 00701343
  Hugo López-Fernández authored Sep 28, 2022
  
  00701343
Sep 27, 2022
- Initial commit of the project · ea18a032
  Hugo López-Fernández authored Sep 27, 2022
  
  ea18a032