nxn

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

December 2023

Detecting scRNA-seq study duplicates using sentence embeddings

I have been maintaining a spreadsheet of publications that generated single-cell transcriptomics data for about five years.

Dec 1, 2023 • 

Valentine Svensson

October 2023

Interpreting scVI - adjusted expression levels

With single cell RNA-seq measurements, you observe molecule counts spread over genes of origin from a sample of the transcripts in individual cells.

Oct 5, 2023 • 

Valentine Svensson

September 2023

Lyft priority pickup waiting times

When I moved to California at the beginning of the year I didn’t have a drivers’ license.

Sep 21, 2023 • 

Valentine Svensson

Training scVI — Summarizing posterior predictive distributions

How good is a trained scVI model?

Sep 6, 2023 • 

Valentine Svensson

August 2023

Training scVI - Posterior predictive distributions over epochs

When fitting an scVI model for scRNA-seq data it is important to inspect the loss curves over epochs after finishing training.

Aug 13, 2023 • 

Valentine Svensson

June 2023

Tutorial - Label transfer with scVI and scHPL

One of the most time-consuming and challenging steps in single-cell RNA-seq analysis is the assignment of cell types based on clustering marker genes.

Jun 9, 2023 • 

Valentine Svensson

May 2023

Cells in the center of scVI latent space

When modeling scRNA-seq data with scVI, it is common to notice that some cells of mixed cell types appear in the center of the representation space.

May 24, 2023 • 

Valentine Svensson

March 2023

Keyboard switches on a Squarp Pyramid MIDI sequencer

Over the last couple of years I have gotten interested in synthesizers and electronic music.

Mar 2, 2023 • 

Valentine Svensson