Document GEO and RNA-seq ingestion pipelines, fix stale v109 references - #120
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sgiannouk wants to merge 7 commits into
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Document GEO and RNA-seq ingestion pipelines, fix stale v109 references#120sgiannouk wants to merge 7 commits into
sgiannouk wants to merge 7 commits into
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The downloader and geo_download.py defaults already moved to v115; the README text still described v109.
Links the GEO download pipeline into the main workflow docs, and pulls in the RNA-seq pipeline summary and canonical DE schema notes that main already documents but this branch's README predates.
Per the RNA-seq pipeline maintainer.
Mirrors the GEO download pipeline README's format: overview diagram, numbered steps, output schema, and an outputs table.
Moves detailed RNA-seq ingestion mechanics into pipelines/experiments/README.md and leaves a brief pointer in the main README. Renumbers the remaining Workflow steps and repoints the GEO README's step 5 at the new dedicated doc.
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Summary
geo_download.py, and fix the resulting stale v109 mentions across the GEO and main READMEsmain(OE/KO->Overexpression/Knockout/Knockdown) by cherry-picking upstream's own rename commitpipelines/experiments/README.mdfor the RNA-seq ingestion pipeline (same format as the GEO README), and slim the main README's experiment section down to a short pointercontrol_mean_normalized_countin the canonical DE schema, per the RNA-seq pipeline maintainerCloses #119
Test plan
v109references in touched docs