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Paper2Agent_decoupleRpy

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Paper2Agent_decoupleRpy / scripts

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6 contributors

History: 16 commits

avoigt1121

scripts: add WIP cptac_pda_counts (raw-counts/Path A) assembly script

edd48ca 2 months ago

_gse205154_sears_common.py

8.57 kB
scripts: pin BIODATA_REGISTRY_COMMIT to 533906d for GSE205154 provenance 2 months ago
_investigate_gpl6244.py

2.04 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months ago
_precompute_common.py

11.4 kB
Switch GPL platform annotation to NCBI .annot.gz instead of _family.soft.gz 3 months ago
_verify_precompute.py

2.51 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months 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

4.84 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_cptac_pda_counts.py

15.1 kB
scripts: add WIP cptac_pda_counts (raw-counts/Path A) assembly script 2 months ago
assemble_gse15471.py

4.81 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse16515_mayo.py

2.69 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months ago
assemble_gse17891.py

3.98 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse205154_sears.py

1.08 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse205154_sears_counts.py

1.37 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse205154_sears_tmm.py

1.19 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse21501.py

4.26 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse28735_pdac.py

3.02 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months ago
assemble_gse57495.py

4.47 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_gse62165_jiang.py

2.33 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months ago
assemble_gse71729_moffitt.py

1.83 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months ago
assemble_gse71989_chen.py

2.3 kB
Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin 3 months ago
assemble_nones.py

3.97 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months ago
assemble_paca_ca.py

4.8 kB
scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo 2 months 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

3.76 kB
Bump biodata-registry pin to 3bf0eb9; add Nones symbol-fix script 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

4.8 kB
Lint cleanup: remove unused imports, empty f-strings, split import lines 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

453 Bytes
Add scripts/requirements-dev.txt for curation-script deps 2 months ago
security_scan.sh

2.89 kB
Stage: pinned deps, API-key fallback, apt probe, security scan 2 months ago
test_limma_runtime.py

884 Bytes
Add PDAC dataset adapter, workflow, semantic, and analysis layers 4 months ago