A practical guide to finding genes that change between conditions in multi-sample single-cell RNA-seq — the correct way. See why per-cell tests like Seurat’s FindMarkers inflate false positives on cro...

You Can Change Your Appetites Linear algebra, statistics, machine learning—these used to feel abstract to me. I had zero experience of bioinformatics when I was studying my PhD in a wet lab. I memorized formulas without truly understanding them. But over time, I found the right resources that made these concepts click, especially in the context of bioinformatics. I wrote a blog post: My opinionated selection of books/urls for bioinformatics/data science curriculum six years ago, and many links are broken.

:microscope: Path to a free self-taught education in Bioinformatics! - ossu/bioinformatics

I was asked this question very often: “Tommy, what’s the p-value cutoff should I use to determine the differentially expressed genes; what log2 Fold change cutoff should I use too?” For single-cell RNAseq quality control, what’s the cutoff for mitochondrial content? My answer is always: it depends. I was joking: determining a cutoff is 90% of the work a bioinformatician does. Why is that? Biology is more than just statistics.

The emergence of agency in biomolecular systems involves a biphasic process of communication that constructs a message before it can be transmitted for interpretation. Evolutionary genomic and bioinf....

You Can Change Your Appetites Linear algebra, statistics, machine learning—these used to feel abstract to me. I had zero experience of bioinformatics when I was studying my PhD in a wet lab. I memorized formulas without truly understanding them. But over time, I found the right resources that made these concepts click, especially in the context of bioinformatics. I wrote a blog post: My opinionated selection of books/urls for bioinformatics/data science curriculum six years ago, and many links are broken.