nxn

SCVI with variational batch encoding

For last couple of months I have been exploring batch integration strategies with SCVI and MRVI, and the possibility to optionally disable integration…

Jun 21 • 

Valentine Svensson

May 2025

Evaluating automatic cell number extraction from single cell papers

For the past ~7 years I have been tracking the scale of scRNA-seq experiments in a spreadsheet which we published as the ‘Single Cell Studies Database…

May 26 • 

Valentine Svensson

Merging SCVI models

There are massive amounts of single-cell RNA-seq data, and data is still being produced.

May 21 • 

Valentine Svensson

April 2025

An attempt at speeding up TSNE using Apple MLX

I’m often encountering situations where I want to do a quick 2D visualization of some data.

Apr 1 • 

Valentine Svensson

March 2025

SCVI — Inference-based optional integration

The batch-integrating SCVI model is a conditional variational autoencoder (cVAE, Sohn et al.

Mar 28 • 

Valentine Svensson

SCVI — Integrating or not?

In modern single cell analysis workflows you fit a model to your data that allow you to ask questions about the data.

Mar 18 • 

Valentine Svensson

Cloud GPUs for SCVI

When I moved last year I decided to get rid of my Windows PC.

Mar 6 • 

Valentine Svensson

The strength of a hand

In this video I model the scaling strengths of the different poker hands in Balatro.

Mar 3 • 

Valentine Svensson

August 2024

February 2024

Immune response enrichment analysis in Python

In a recent paper, Cui and colleagues define a ‘dictionary’ of immune responses to cytokine stimulation (Cui et al.

Feb 12, 2024 • 

Valentine Svensson

Single-cell metadata as language

Single-cell RNA-seq data is molecule counts of transcripts from different genes within different cells.

Feb 4, 2024 • 

Valentine Svensson

January 2024

Organizing scRNA-seq data with LaminDB

Occasionally, when I’m curious about something scRNA-seq related, I analyze some data.

Jan 31, 2024 • 

Valentine Svensson