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dd5ecfc
cpr
89.3 MB
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8 contributors
History:
246 commits
ronboger
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
Safe
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