Any #tiledb #scRNA users out there?

I am ingesting data from an `h5ad` file into a soma with `tiledbsoma.io.from_h5ad` (#python API).

Does this function load the entire h5ad into memory before conversion? Python keeps crashing which I am guessing are OOO issues. If yes, is there another option to do this conversion without loading the data in memory?

It would be strange if the only option is to load the whole thing into memory considering how massive scRNA datasets are these days.

Our #NEIfunded study led by Farhad Farjood, Nathan Boles & Jeffrey Stern reveals heterogeneity of retinal pigment epithelium cells in the human eye using #scRNA-seq & proteomics. We describe unique spatial patterns that suggest functional differences for RPE subpopulations in the eye.

- with S. Nandakumar, T. Bertucci, T. Kiehl, S. Lotz, Yue Wang, J. Black, S. Sai, J. Kozak, B. Arduini and S. Temple

This work was supported by the NIH & Luxa Biotech.

Full text | https://zurl.co/4hwI6

Qing Nie
System learning of single cells

Fascinating talk about analyses of single cell data

Eg paper on angiogenesis in #elife
"Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification"
#ScRNA #cellchat #rna #notch #cellbiology

https://elifesciences.org/articles/89262
https://faculty.sites.uci.edu/qnie/

Pipeline release! nf-core/scnanoseq v1.0.0 - nf-core/scnanoseq v1.0.0 - Titanium Toad!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.0.0

#10xgenomics #long-read-sequencing #nanopore #scrna-seq #single-cell #nfcore #openscience #nextflow #bioinformatics

Getting structurally homogenous spatial samples is often challenging.

We developed a method to map the spatial context of cells between heterogenous samples gaining insights into development and patient sub-populations!

#SpatialBiology #scRNA #compbio

https://www.biorxiv.org/content/10.1101/2024.08.31.610638v1