Repository navigation

dataset: PANTHER Signaling Pathways Collection - #71

Draft

tristan-f-r wants to merge 124 commits into

mainfrom

synthetic-dataset

Draft

dataset: PANTHER Signaling Pathways Collection#71
tristan-f-r wants to merge 124 commits into
mainfrom
synthetic-dataset

Commits on Mar 18, 2026
- chore: drop other datasets
  tristan-f-r
  committed
  b49439e
- Merge branch 'main' into egfr-and-infrastructure
  tristan-f-r
  committed
  2018a13
- chore: re-include
  tristan-f-r
  committed
  136e5ff
- chore: drop tools
  tristan-f-r
  committed
  472468d
- chore: re-add tools
  tristan-f-r
  committed
  a5de971
- dataset: synthetic data
  tristan-f-r
  committed
  50fa813
- docs: cache
  tristan-f-r
  committed
  8ddccb4
- style: fmt
  tristan-f-r
  committed
  90cc277
- docs: on caching
  tristan-f-r
  committed
  eb23b8f
- docs: suggestions from review
  
  tristan-f-r
  and
  ntalluri
  authored
  4b524bc
Commits on Mar 19, 2026
- docs: more comments, refactor: mv function out of Snakefile
  tristan-f-r
  committed
  69fda05
- docs(datasets): mention responsenet and egfr
  tristan-f-r
  committed
  15c7ecb
- docs(datasets): add old synthetic data branch
  tristan-f-r
  committed
  729a51b
Commits on Mar 23, 2026
- chore: mv to scores instead of dmmm
  tristan-f-r
  committed
  922be5d
- docs: drop expiration docs
  tristan-f-r
  committed
  f3d6d41
- docs: clarify snakemake importing
  tristan-f-r
  committed
  a802fde
Commits on Mar 24, 2026
- docs: more clarification on data and files
  tristan-f-r
  committed
  85ba6e9
- refactor: move irefindex back to egfr
  tristan-f-r
  committed
  8139f14
- chore: revert web
  tristan-f-r
  committed
  5a8c02e
- docs: clarify on cache
  tristan-f-r
  committed
  041f998
Commits on Mar 25, 2026
- chore: apply suggestions
  
  tristan-f-r
  and
  ntalluri
  authored
  bd3bcab
- docs: apply suggestions
  tristan-f-r
  committed
  c08a0b8
- chore: apply suggestions
  tristan-f-r
  committed
  b3cf691
- drop extensions
  tristan-f-r
  committed
  193f75a
- refactor(egfr): correctly specify output dirs
  tristan-f-r
  committed
  0581bea
Commits on Mar 26, 2026
- feat(egfr): add target nodes, fmt
  tristan-f-r
  committed
  320aa87
- feat: archived biomart url
  tristan-f-r
  committed
  f696c6d
- docs: apply suggestion
  
  tristan-f-r
  and
  ntalluri
  authored
  998030b
- docs: apply more suggestions, fix config, unfix magic value
  tristan-f-r
  committed
  040a62e
- Merge branch 'egfr-and-infrastructure' of https://github.com/Reed-CompBio/spras-benchmarking into egfr-and-infrastructure
  tristan-f-r
  committed
  c18d841
- move contributing over
  tristan-f-r
  committed
  0063ae2
- chore: mv
  tristan-f-r
  committed
  bf55684
- fix up references
  tristan-f-r
  committed
  794e8ae
- refactor: use ensp name
  tristan-f-r
  committed
  e6bf86b
Commits on Apr 7, 2026
- clean up on docs
  tristan-f-r
  committed
  6b4841a
Commits on Apr 15, 2026
- fix(tools): re-introduce trim.py
  tristan-f-r
  committed
  d366409
Commits on Apr 20, 2026
- docs: update err msg
  tristan-f-r
  committed
  7922f06
- chore: address some comments
  tristan-f-r
  committed
  d5b295d
Commits on Apr 21, 2026
- feat: allow for version aliasing
  tristan-f-r
  committed
  801b3c6
- Merge branch 'egfr-and-infrastructure' of https://github.com/Reed-CompBio/spras-benchmarking into egfr-and-infrastructure
  tristan-f-r
  committed
  6d2c7df
- docs: mention v12 in the file name
  tristan-f-r
  committed
  ef1773b
- docs: mention aliasing
  tristan-f-r
  committed
  0c6d6f0
- feat: uncompressing zip files
  tristan-f-r
  committed
  c2d17db
- test: setup with directory redirects
  tristan-f-r
  committed
  66de95b
- feat: deduplicate edges of output interactome
  tristan-f-r
  committed
  d4749e7
- chore: mv directory test
  tristan-f-r
  committed
  b5e6332
- fix: add init file to cache tests
  tristan-f-r
  committed
  dbba053
- docs: apply suggestions
  tristan-f-r
  committed
  f8ce2a8
- docs: cache
  tristan-f-r
  committed
  8a51052
- fix: designate cache & tools as modules
  tristan-f-r
  committed
  69de55b
- docs: general egfr cmts, fix: make egfr dataset work
  tristan-f-r
  committed
  df4a16e
Commits on Apr 23, 2026
- feat: actual interactome trimming
  tristan-f-r
  committed
  a178a2a
- style: fmt
  tristan-f-r
  committed
  5df4a13
Commits on Apr 29, 2026
- style: fmt
  tristan-f-r
  committed
  5e13705
- fix: address larger notes
  tristan-f-r
  committed
  b5ddaa4
- docs: fix outdated comments, apply some minor suggestions
  tristan-f-r
  committed
  cd41227
- chore: more minor suggestions
  tristan-f-r
  committed
  38ef456
- chore: apply suggestions
  tristan-f-r
  committed
  b6b958e
Commits on Apr 30, 2026
- refactor: change file name
  tristan-f-r
  committed
  5f6720c
- chore: apply suggestions
  tristan-f-r
  committed
  8755803
- fix: set header=False for normalized interactome
  tristan-f-r
  committed
  c7efcba
- refactor: use other prize value
  tristan-f-r
  committed
  1b60dcb
Commits on May 4, 2026
- refactor: move config to egfr
  tristan-f-r
  committed
  fc09ffb
- ci: use EGFR for config name
  tristan-f-r
  committed
  5837d7f
Commits on May 5, 2026
- ci: add uv environment tests
  tristan-f-r
  committed
  1ec407e
Commits on May 14, 2026
- update the deduplicate tool function, remove normalize function and be direct
  ntalluri
  committed
  5276687
- remove concept of latest
  ntalluri
  committed
  3006983
- precommit
  ntalluri
  committed
  3f69499
- fix tools test
  ntalluri
  committed
  7595652
- cleanup
  ntalluri
  committed
  1f0ca12
- precommit
  ntalluri
  committed
  78c0adf
- add todo
  ntalluri
  committed
  e682f09
- update trim_input_nodes.py, it was an & and it needed to be an |
  ntalluri
  committed
  230a765
- update comment and precommit
  ntalluri
  committed
  b0a3165
Commits on May 21, 2026
- Merge branch 'egfr-and-infrastructure' into synthetic-dataset
  ntalluri
  committed
  d223e1b
- got this back to a working state
  ntalluri
  committed
  3022157
- precommit
  ntalluri
  committed
  7f2724d
- make workflow work
  ntalluri
  committed
  c61f5ee
- start of restructure
  ntalluri
  committed
  6c9debd
- add in physical links
  ntalluri
  committed
  311de92
- todo
  ntalluri
  committed
  5d62559
- comments
  ntalluri
  committed
  4802a14
- Merge branch 'egfr-and-infrastructure' into synthetic-dataset
  ntalluri
  committed
  d091ccd
Commits on May 26, 2026
- restructuing
  ntalluri
  committed
  cf9f183
Commits on Jun 1, 2026
- start of restructure
  ntalluri
  committed
  12825ed
- working on processing the pathways and figuring out id mapping
  ntalluri
  committed
  72507f7
- changed to using ensp, cleaned up processing a pathway, cleaned up interactome, added start of processing input nodes
  ntalluri
  committed
  d4db7a0
- precommit and remove files that are not needed
  ntalluri
  committed
  67f6997
- update snakefile
  ntalluri
  committed
  a8d431a
- remove old interactome script, add new one, update snakefile, and add in mkdirs
  ntalluri
  committed
  1ecdca0
- added the code for processing the input nodes
  ntalluri
  committed
  2a1cba8
- many different changes
  ntalluri
  committed
  cf6136e
- fix a mistake for the trimming
  ntalluri
  committed
  ef4bdcb
Commits on Jun 2, 2026
- starting to change threhsold
  ntalluri
  committed
  e90844d
- still working on this
  ntalluri
  committed
  da892db
- trying to debug the sampling
  ntalluri
  committed
  67aaed5
- precommit
  ntalluri
  committed
  fc98941
Commits on Jun 5, 2026
- finished a draft of threshold interacotmes and add in pathway statistics to main scripts
  ntalluri
  committed
  ef2ad2a
- remove old files and add in new ones
  ntalluri
  committed
  e8c8879
- started on config file
  ntalluri
  committed
  c2c4f3f
- in progress
  ntalluri
  committed
  3cdc2ea
- precommit
  ntalluri
  committed
  b559537
Commits on Jun 9, 2026
- redid thresholded interactomes and think more through the upsampled interactomes and get a better idea on what to do
  ntalluri
  committed
  0b3e391
- precommit
  ntalluri
  committed
  50da408
Commits on Jun 10, 2026
- draft of upsample pathways
  ntalluri
  committed
  91b2acf
- precommit
  ntalluri
  committed
  bad4a89
- revert some of the precommit and clean up
  ntalluri
  committed
  6987c6a
- update code
  ntalluri
  committed
  dee0246
- trying to remove typos problem with precommit
  ntalluri
  committed
  0c78bdc
- more attempts
  ntalluri
  committed
  6f1f8fe
- removed upsample from typos
  ntalluri
  committed
  83f5286
- remove the extra stuff added
  ntalluri
  committed
  9ca34fe
Commits on Jun 11, 2026
- new edits to thresholding to write even if doesn't pass properties
  ntalluri
  committed
  2cdf2c9
- redid the thresholding code
  ntalluri
  committed
  41714c6
- fixed a bug
  ntalluri
  committed
  30efad7
Commits on Jun 12, 2026
- added a final threhsold piece of code, fixed a bug in pc-panther-biopax
  ntalluri
  committed
  f787d48
- fix run_snakemake.sh?
  ntalluri
  committed
  d7fe458
Commits on Jun 15, 2026
- update data to what we are actually using
  ntalluri
  committed
  3f853aa
- precommit
  ntalluri
  committed
  82b1a05
Commits on Jun 17, 2026
- updated code
  ntalluri
  committed
  e8a3476
Commits on Jun 23, 2026
- add code for zip the interactomes
  ntalluri
  committed
  9dd1455
- update zipping code for interactomes
  ntalluri
  committed
  39212f5
- rename file
  ntalluri
  committed
  f5dad23
Commits on Jul 22, 2026
- update the interactome
  ntalluri
  committed
  cde9e4c

Commits

Commits on Mar 18, 2026

Commits on Mar 19, 2026

Commits on Mar 23, 2026

Commits on Mar 24, 2026

Commits on Mar 25, 2026

Commits on Mar 26, 2026

Commits on Apr 7, 2026

Commits on Apr 15, 2026

Commits on Apr 20, 2026

Commits on Apr 21, 2026

Commits on Apr 23, 2026

Commits on Apr 29, 2026

Commits on Apr 30, 2026

Commits on May 4, 2026

Commits on May 5, 2026

Commits on May 14, 2026

Commits on May 21, 2026

Commits on May 26, 2026

Commits on Jun 1, 2026

Commits on Jun 2, 2026

Commits on Jun 5, 2026

Commits on Jun 9, 2026

Commits on Jun 10, 2026

Commits on Jun 11, 2026

Commits on Jun 12, 2026

Commits on Jun 15, 2026