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89.3 MB

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8 contributors

History: 246 commits

ronboger's picture

Claude Opus 4.5

chore: clean up redundant scripts and consolidate thresholds

dd5ecfc 3 months ago

data
data: add JCVI Syn3.0 test sequences with documentation 3 months ago
docs
refactor: cleanup repo, add SLURM scripts, document reproducibility 3 months ago
notebooks
chore: clean up redundant scripts and consolidate thresholds 3 months ago
protein_conformal
refactor: consolidate CLI to single 'cpr search' command 3 months ago
results
chore: clean up redundant scripts and consolidate thresholds 3 months ago
scripts
chore: clean up redundant scripts and consolidate thresholds 3 months ago
tests
fix: update CLI tests for --input flag and --no-filter 3 months ago
.dockerignore

18 Bytes
created dockerfile and dockerignore 9 months ago
.gitattributes

170 Bytes
Initial commit about 2 years ago
.gitignore

3.99 kB
chore: clean up redundant scripts and consolidate thresholds 3 months ago
CLAUDE.md

11.6 kB
feat: add FNR threshold computation and partial match support 3 months ago
DATA.md

4.39 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 3 months ago
DEVELOPMENT.md

7.92 kB
fix: use correct calibration dataset (pfam_new_proteins.npy) 3 months ago
Dockerfile

1.46 kB
refactor: cleanup repo, add SLURM scripts, document reproducibility 3 months ago
GETTING_STARTED.md

13.3 kB
chore: clean up redundant scripts and consolidate thresholds 3 months ago
LICENSE

11.4 kB
Update LICENSE almost 2 years ago
README.md

9.15 kB
feat: add one-step cpr find command and FDR-level search 3 months ago
REPO_ORGANIZATION.md

7.53 kB
docs: add comprehensive REPO_ORGANIZATION.md 3 months ago
SESSION_SUMMARY.md

4.77 kB
docs: add session summary of cleanup work 3 months ago
TEST_SUMMARY.md

6.08 kB
feat: add CLEAN embedding support and CLI tests 3 months ago
UPLOAD_CHECKLIST.md

4.82 kB
feat: add one-step cpr find command and FDR-level search 3 months ago
apptainer.def

3.02 kB
docs: improve Apptainer usage instructions 3 months ago
docker-compose.yml

540 Bytes
chore: add docker-compose.yml for easier deployment 3 months ago
environment.yml

1.62 kB
edited dockerfiles 9 months ago
pyproject.toml

2.44 kB
refactor: cleanup repo, add SLURM scripts, document reproducibility 3 months ago
requirements.txt

557 Bytes
refactor: cleanup repo, add SLURM scripts, document reproducibility 3 months ago
setup.py

128 Bytes
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 3 months ago