EuroBioC 2025 — Tools¶
EuroBioC2025 ran 5 keynotes + ~25 short talks + 5 hands-on workshops + posters. Most short talks introduce or update a Bioconductor package — that's what this directory captures. Each entry below corresponds to one package presented at EuroBioC2025.
Status: Template stub. We're proposing the per-tool format here for review before bulk extraction. Once locked, ~30 entries get populated from the talk + workshop list.
Per-tool entry template¶
Each tool gets its own page (tools/<package-slug>.md) following this structure:
# <PackageName>
**One-line description** — what the package does in plain language.
- **Maintainer:** <name> (<institution>)
- **Bioconductor:** [package page]
- **Source:** [GitHub link]
- **Vignette:** [vignette link]
- **Status at EuroBioC2025:** new release / major update / methods talk / case study / workshop
## Talk at EuroBioC2025
- **Speaker:** ...
- **Day / session:** ...
- **Slides:** [Zenodo DOI]
- **Video:** [YouTube link if recorded]
- **Abstract / talk page:** [conf-site link]
## What it does
2–3 sentences: the problem it solves, key methodological idea, what it consumes/produces.
## Where it fits in the corpus
- AACR 2026: [link if mentioned]
- ISMB 2026: [link if mentioned]
- RECOMB 2026: [link if mentioned]
- Nextflow Summit 2026: [link if mentioned]
- GBCC 2025: [link if mentioned]
## Notes
Free-form impressions, benchmarks claimed, comparisons to alternatives.
Tool index¶
23 entries covering EuroBioC2025 short talks + workshops, ordered by day and session. Three were drafted by hand to set the template (DESpace, DeeDeeExperiment, iSEE); the remaining 20 came from a single bulk pass after the format was validated. Slide DOIs are TBD — the Bioconductor community typically deposits to Zenodo within a few weeks of the meeting.
Skipped (not in this table): community / non-package talks (Laurah Ondari on Bioconductor training in Africa; Katharina F. Heil on ELIXIR resources), three short talks without a clear package anchor (Lucas Beerland — distributional inference single-cell proteomics; Jiayi Wang — ATAC-seq bias correction; Ilaria Billato — histopathological image integration). Six keynotes are deferred to a separate digest pass.
| Package | Domain | Speaker | Day | Slides | Video | Mentioned elsewhere |
|---|---|---|---|---|---|---|
| notame | metabolomics | Vilhelm Suksi | Day 1 (AM) | TBD | not recorded | Metabonaut |
| Metabonaut | metabolomics (tutorial) | Philippine Louail | Day 1 (AM) | TBD | not recorded | notame, SpectriPy |
| omicsGMF | dim. reduction | Lieven Clement | Day 1 (AM) | TBD | not recorded | msqrob2, iSEE |
| miaTime | microbiome (time series) | Geraldson T. Muluh | Day 1 (AM) | TBD | not recorded | mia |
| SpectriPy | mass spec (cross-lang) | Johannes Rainer | Day 1 (AM) | TBD | not recorded | Metabonaut |
| RCX | networks | Florian Auer | Day 1 (AM) | TBD | not recorded | — |
| scp-distributional | single-cell proteomics | Lucas Beerland | Day 1 (AM) | TBD | not recorded | msqrob2, omicsGMF |
| MIRit | miRNA-mRNA | Jacopo Ronchi | Day 1 (PM) | TBD | not recorded | MOSClip |
| DeeDeeExperiment | infra / data class | Najla Abassi | Day 1 (PM) | TBD | not recorded | iSEE |
| edgeR | RNA-seq DE | Lizhong Chen | Day 1 (PM) | TBD | not recorded | DESpace |
| MOSClip | multi-omics survival | Anna C E De Lima Tanada | Day 1 (PM) | TBD | not recorded | MIRit |
| Rega | EGA submission | Igor Cervenka | Day 1 (PM) | TBD | not recorded | — |
| footprintR | epigenomics | Charlotte Soneson | Day 2 (AM) | TBD | not recorded | — |
| decemedip | methylation deconvolution | Ning Shen | Day 2 (AM) | TBD | not recorded | — |
| atacseq-biascorrection | ATAC-seq bias correction | Jiayi Wang | Day 2 (AM) | TBD | not recorded | — |
| SpatialData | spatial omics (Python) | Luca Marconato | Day 2 (late AM) | TBD | not recorded | OSTA, DESpace |
| DESpace | spatial DE | Peiying Cai | Day 2 (late AM) | TBD | not recorded | edgeR, spatialFDA |
| spatialFDA | spatial multi-sample | Martin Emons | Day 2 (late AM) | TBD | not recorded | DESpace |
| consICA | ICA / signal decomp. | Maryna Chepeleva | Day 2 (late AM) | TBD | not recorded | omicsGMF |
| barbieQ | clonal tracking | Liyang Fei | Day 2 (late AM) | TBD | not recorded | — |
| HistoImagePlot | histopath image integration | Ilaria Billato | Day 2 (late AM) | TBD | not recorded | OSTA |
| OSTA | spatial omics (book) | Dong & Patrick | Day 2 (workshop) | TBD | not recorded | DESpace, SpatialData |
| mia | microbiome | Tuomas Borman | Day 2 (workshop) | TBD | not recorded | miaTime |
| msqrob2 | proteomics | Christophe Vanderaa | Day 2 (workshop) | TBD | not recorded | omicsGMF |
| Workshop Platform | infrastructure | Alexandru Mahmoud | Day 2 (workshop) | TBD | not recorded | iSEE |
| iSEE | visualization | Federico Marini | Day 2 (workshop) | TBD | not recorded | DeeDeeExperiment |
Why this format¶
- Cross-vault links matter — this is the only place where "tool released here, used in cancer-research talk X, benchmarked in methods paper Y" can be one click apart
- Slides + video + vignette + Bioconductor page in one place — none of the other vaults have this complete quartet
- Domain field lets the table slice by single-cell / spatial / etc. without duplicating into topic pages
- Status field tells a reader at a glance whether they're looking at a v1.0 announcement or a 4-year-old package's annual update
Open questions for the pilot¶
- Granularity — ✅ locked: one page per tool
- AACR dossier mirroring — ✅ locked: full entry in both vaults, cross-linked (no canonical/stub asymmetry)
- Sample tools to draft first — ✅ done: DESpace / DeeDeeExperiment / iSEE drafted; the DDE ↔ iSEE pair exercises the cross-vault link mechanic
- Edge case: non-Bioconductor tools — open: SpatialData (Marconato Day 2 talk) is Python-primary with R interop in development. The current template assumes a Bioconductor package page. Need a variant for cross-language or pre-release tools — proposed: a "Status: external / pre-release" badge that swaps the Bioconductor field for "(Python-primary; R interop layer in development)" plus a link to the upstream framework