Kenny Pavan

0's and 1's; Purines and Pyrimidines.
Plant Based, Climber, #Trekkie, #OHSU PhD Student
myOwnOpinions=true

[Arpiar Saunders, PhD @your_arpy]

@kennypavan's AnnSQL software for facile, lightning-fast analysis of large-scale scRNA-seq datasets is out now in @BioinfoAdv. >19k downloads thus far and we'd love to grow the developer base. Easily analyze millions of RNA profiles from your laptop. No HPC necessary!

[Kenny Pavan @kennypavan]

Let's talk about inte𝗥operability. The Python based AnnSQL package creates shareable databases from AnnData objects. Using the DuckDB R package, you can easily open these databases and query the database 🧬🖥️ #SingleCell #R #bioinformatics #DuckDB

https://t.co/uJfxL8mupX

[Arpiar Saunders, PhD @your_arpy]

Our latest work in collaboration with the Bourhy Lab (Pasteur Inst.) in which we use scRNA-seq to characterize host-rabies molecular interactions across diverse human brain cell types. Recommended if you're interested in "system virology" or glial biology: https://t.co/jPhuG3z3SL

[Kenny Pavan @kennypavan]

https://t.co/njSqBSpm26

[Kenny Pavan @kennypavan]

New feature in #AnnSQL!

Easily create meta cell views for massive single-cell datasets. In this example: 600k cells are grouped by type & age to provide a summary of molecular diversity.

Live long and analyze🖖#Bioinformatics #DuckDb #Genomics

https://t.co/EbMaVhLYYt

[Kenny Pavan @kennypavan]

@tom_doerr Wildly helpful! 🙏

[Kenny Pavan @kennypavan]

Huge thanks to my mentor @your_arpy, @OHSU_BME, @VollumInstitute, and @OHSUSOM for their support!

[Kenny Pavan @kennypavan]

With AnnSQL, the needs of the many cells outweigh the needs of the few. Achieve warp-speed insights across millions of data points! 🖖#spock #bioinformatics #datascience #duckdb #annsql

https://t.co/njSqBSpm26

[Kenny Pavan @kennypavan]

We pushed AnnSQL to its limits with a 4.4 million-cell mouse brain dataset 🧠 and it excelled! Filtering alone was 680x faster than standard filtering of AnnData on a laptop.

[Arpiar Saunders, PhD @your_arpy]

Struggling with AnnData? Meet AnnSQL, our python package for lightning-fast scRNA-seq analysis:
https://t.co/Le6NMxwtJc
AnnSQL achieves ~700x runtime improvements over AnnData, enabling datasets with millions of cells to be queried in minutes on a laptop using elegant SQL syntax.

[Kenny Pavan @kennypavan]

@markahix @levarburton @Marina_Sirtis This post... projects thoughtfulness and dignity 🤖🤠😂

[Kenny Pavan @kennypavan]

@ATinyGreenCell @Twitch

[Kenny Pavan @kennypavan]

Stumbled upon this project shortly after watching Dune. Can't help but wonder if this model accepts a spice level parm? 🤔

https://t.co/UCT6BEPXRA

[Kenny Pavan @kennypavan]

@markahix Glory to you and your house!

[Kenny Pavan @kennypavan]

@markahix @CompChemBioBot Or, something is broken😂

[Kenny Pavan @kennypavan]

Things are now in motion that cannot be undone.

#Bioinformatics

[Kenny Pavan @kennypavan]

Anyone else watching Star Trek Deep Space Nine S6E26? 🖖