BRC-Analytics collaboration

## Objective
Leverage Teresa O'Meara's expertise to develop turn-key Galaxy analyses for the fungal research community, focusing on RNAseq and pangenome analyses for BRC-analytics.org

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> [!WARNING]
> The list below is more of a sanity check as it more reliable than @nekrut's brain

## Agenda

### 1. Pangenome Analysis Strategy
**Discussion:**
- [ ] Review Teresa's C. auris pangenome work and data sharing timeline
- [ ] Explain HPRC collaboration and cutting-edge pangenome tools (vg giraffe, DeepVariant, ODGI) (also see https://www.nature.com/articles/s41592-024-02407-2, https://www.nature.com/articles/s41592-024-02430-3, and https://www.nature.com/articles/s41592-024-02402-7)
- [ ] Discuss adapting these tools as standards for yeast/fungal pangenome studies

**Action Items:**
- [ ] **Teresa:** Provide C. auris pangenome data specs and preferred reference assembly (after manuscript submission)
- [ ] **Anton:** Share draft workflow designs showing HPRC tools adapted for fungal pangenomes
- [ ] **Both:** Define 2-3 pilot use cases for fungal pangenome analysis

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### 2. RNAseq Best Practices & Workflow Development
**Discussion:**
- [ ] Review Teresa's current pipeline (Kallisto + DESeq2)
- [ ] Present Galaxy workflows designed based on Teresa's earlier papers
- [ ] Discuss packaging as community best practices + potential methods paper

**Action Items:**
- [ ] **Anton:** Share draft Galaxy RNAseq workflows for review
- [ ] **Teresa:** Provide feedback on workflows
- [ ] **Teresa:** Identify 2-3 representative datasets for testing
- [ ] **Teresa:** Suggest key RNAseq scenarios for fungal research (differential expression, time series, etc.)
- [ ] **Both:** Outline scope for methods paper on standardized fungal RNAseq analysis

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### 3. Gene Co-expression Network Visualization
**Discussion:**
- [ ] Status update on C. albicans and C. neoformans co-expression data integration
- [ ] Confirm genome reference (Assembly 22/ASM18296v3)

**Action Items:**
- [ ] **Anton:** Complete co-expression network integration with UCSC Genome Browser
- [ ] **Anton:** Provide demo link for Teresa's review

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### 4. CGD Integration & Community Coordination
**Discussion:**
- [ ] Strategy for syncing BRC-analytics.org with Candida Genome Database (CGD)
- [ ] Navigation advice for fungal research community

**Action Items:**
- [ ] **Teresa:** Provide introduction/guidance for approaching Gavin Sherlock (CGD)
- [ ] **Teresa:** Suggest key stakeholders to engage early
- [ ] **Anton:** Draft CGD integration collaboration proposal

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### 5. Next Steps & Timeline
**Action Items:**
- [ ] Schedule follow-up meeting (4-6 weeks)
- [ ] Establish regular check-ins during C. auris manuscript prep
- [ ] Create shared document for tracking use cases and workflow requirements

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## Context
**Related Email Threads:**
- Pangenome Tools (Oct 9-17, 2025)
- Hosting Pangenome + gene coexpression data (Aug 28 - Oct 21, 2025)
- RNAseq + Pangenome (Oct 22-24, 2025)

**Key Background:**
- Teresa has C. auris pangenome ready (manuscript in prep, available in ~few months)
- Current RNAseq pipeline: Kallisto + DESeq2
- Co-expression data: C. albicans (CalCEN) and C. neoformans datasets provided
- Need integration with CGD (contact: Gavin Sherlock)

The issue names no repository files, tests, or entry points. Start by clarifying which workflow or integration is the intended deliverable, identifying its repository location, and defining the pilot datasets and acceptance criteria before implementation begins.

Written by the indexing model from the issue text.