---
# System prepended metadata

title: '2022-03-04: Bioconductor formats'
tags: [' meeting', ' data interchange', scverse]

---

---
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