---
tags: scverse, data interchange, meeting
---

# 2022-03-04: Bioconductor formats

*Attendees:* Robert Gentleman, Wolfgang Huber, Ludwig Geistlinger, Roger , Danila, Ilia, Martin, Luke

## Agenda

* The single-cell-data/matrix-api that Ambrose has been organizing
* Are you fully bought in here? Thoughts on the model? Thoughts on TileDB?
* Collaboration between Zelkonverter and the MuData bioconductor packages
* How Seurat fits in here. Are there barriers to shared IO libraries in the R ecosystem?

## Notes

* Robert
* Running center for comp bio medicine
* Bioconductor + structured data
* Interchange
* Ludwig Geistlinger (in Robert's lab)
* scrna-seq + spatial
* Roger (w/ robert)
* Genomics +
* Wolfgang
* At embl,
* Martin
* Lead bioconductor in the past
* Very interested in data interchange
* Luke
* Want to work across both
* Zelkonverter
* Qs
* Spatial datastructures?

* Thoughts on the matrix API
* HDF5
* Access
* Bundling of a compression library
* TileDB
* Like the compression, and being cloud ready
* Zarr
* Spatial
* Pretty large
* OME-ngff
* LAPACK, TACO
* Niels Gehlenborg
* vitessce
* netcdf in R
* Scope of experiment hub
* Ludwig data packages
* ExperimentHub formats
* What do you need to encapsulate in the class
* OME
* Arrow missing values
* Masks seem okay
* Marcel Ramos and Levi Waldron
* Multiomics
* Genomic ranges
* Multi-exon rows aren't covered in python
* But are they used much in R
* Multi-assay experiment
* vs purpose built, like archR

Follow up:

* How do we work on interchange?
* consortium model? with funding?
* From bioconductor
* Multiomics - Check with Levi
* Feature object matrix group
* We could present to technical advisory board
* Vince
* PPI packages
* Coordinated
* Tximeta
* Distributing data with documentation
* Email back
* https://github.com/ccb-hms/BioPlexPy
* https://bioconductor.org/packages/release/bioc/html/BioPlex.html