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Paper2Agent_decoupleRpy

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Paper2Agent_decoupleRpy / scripts

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History: 30 commits

Annie Voigt

fix(hooks): chain git-lfs pre-push after the ADR-0014 security scan

337d58c 13 days ago

hooks
fix(hooks): chain git-lfs pre-push after the ADR-0014 security scan 13 days ago
_gse205154_sears_common.py
8.57 kB
refactor: tighten invariant-length zips to strict=True (B905) about 2 months ago
_investigate_gpl6244.py
2.04 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
_precompute_common.py
11.8 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
_verify_precompute.py
2.58 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
_vst_transform.R
1.49 kB
feat(sears): assemble scripts for gse205154 vst + filtered_tmm siblings about 2 months ago
analyze_post_analysis_reads.py
9.96 kB
feat(metrics): instrument n_post_analysis_reads to test the 808b91d claim 19 days ago
annotate_gse17891_collisson_subtypes.py
6.51 kB
Add scripts/requirements-dev.txt for curation-script deps 2 months ago
assemble_cptac_pda.py
4.92 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_cptac_pda_counts.py
15.5 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse15471.py
4.86 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse16515_mayo.py
2.76 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse17891.py
3.98 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse205154_sears.py
1.08 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse205154_sears_counts.py
1.37 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse205154_sears_filtered_tmm.py
3.03 kB
feat(sears): assemble scripts for gse205154 vst + filtered_tmm siblings about 2 months ago
assemble_gse205154_sears_tmm.py
1.19 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse205154_sears_vst.py
4.85 kB
feat(sears): assemble scripts for gse205154 vst + filtered_tmm siblings about 2 months ago
assemble_gse21501.py
4.28 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse28735_pdac.py
3.04 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse57495.py
4.61 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse62165_jiang.py
2.39 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse71729_moffitt.py
1.84 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_gse71989_chen.py
2.36 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_myc_kd_kmc_mouse.py
6.86 kB
feat(upload): assemble raw counts/TPM/metadata into an h5ad inside the gate 14 days ago
assemble_nones.py
3.98 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
assemble_paca_ca.py
4.86 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
check_limma_runtime.py
885 Bytes
chore(scripts): rename the limma probe so pytest stops collecting it 19 days ago
extract_paca_ca.R
1.52 kB
Add TCGA-PAAD scoping doc, dataset assembly scripts, ignore .claude/ 3 months ago
fix_gse50827_nones_symbols.py
3.75 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
generate_hgnc_cache.py
1.69 kB
fix: resolve CollecTRI TF symbols + restore igraph network plot 2 months ago
inspect_nones.R
1.76 kB
Add TCGA-PAAD scoping doc, dataset assembly scripts, ignore .claude/ 3 months ago
install_r_packages.R
349 Bytes
Add PDAC dataset adapter, workflow, semantic, and analysis layers 4 months ago
load_and_validate_geo.py
4.84 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
precompute_collapsed_h5ads.py
4.72 kB
Add probe-collapse precompute Phase 2 (collapsed_url support) 2 months ago
requirements-dev.txt
455 Bytes
chore(deps-dev): update xlrd requirement from >=2.0 to >=2.0.2 (#6) about 2 months ago
security_scan.sh
9.43 kB
chore(security): make SBOM generation deterministic 22 days ago
verify_s3_sink.py
5.83 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago