Boostrap new project #12
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New project generation works New reports generated for Perplexity auto run Limited conversion due to schema issues Next step - generate from langpa json - with citations.
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Pull request overview
This PR bootstraps a new project focused on analyzing glioblastoma gene programs. The changes introduce automated deep search results from Perplexity AI and comparison data structures for gene program analysis across different glioblastoma cell states.
Key changes:
- Addition of automated deep search analysis files for 14 glioblastoma metamodules
- Introduction of comparison data structures mapping gene programs to Gene Ontology terms
- Creation of embedding index files for program and component organization
Reviewed changes
Copilot reviewed 27 out of 97 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| deepsearch/glioblastoma_perplexity_auto/14_OPC_AC_like_2/run_1.md | Incomplete automated analysis output with truncated JSON |
| deepsearch/glioblastoma_perplexity_auto/13_OPC_like_2/run_2.md | Complete automated gene program analysis for OPC-like cells |
| deepsearch/glioblastoma_perplexity_auto/13_OPC_like_2/run_1.md | Comprehensive markdown report on oligodendroglial gene programs |
| deepsearch/glioblastoma_perplexity_auto/12_NPC_neuronal_like_3/run_2.md | JSON-formatted gene program analysis for neuronal-like cells |
| data/glioblastoma_perplexity_manual/comparison_program_term_matches.csv | Mapping of gene programs to GO terms (row order changes only) |
| data/glioblastoma_perplexity_auto/embeddings_index.csv | New index of 225 gene programs across cell states |
| data/glioblastoma_perplexity_auto/deepsearch_unmatched_programs.csv | New catalog of 84 unmatched gene programs |
| data/glioblastoma_perplexity_auto/deepsearch_skipped_runs.csv | Error tracking for 2 failed analysis runs |
| data/glioblastoma_perplexity_auto/component_embeddings_index.csv | New component taxonomy definitions |
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deepsearch/glioblastoma_perplexity_auto/14_OPC_AC_like_2/run_1.md
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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