Hi! I'm Tommy Tang

Hello Bioinformatics lovers, 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? read the full post here:...

Hello, Bioinformatics lovers, This is Tommy. Usually, you should receive my weekly newsletter on Saturday morning. I was away last week most of the time at Iowa State University https://idgp-biosci-symposium.sites.iastate.edu/2024-speaker-information for a symposium. I loved interacting with the students and seeing the awesome science they were doing. However, biology has become a data-intensive field. Lacking computational skills hinders their ability to analyze their data. Most of the talks...

Hi Bioinformatics lovers, How is your weekend going? We had a leaking toilet, so it is a little hectic with three kids. Anyway, you should expect a newsletter from me every Saturday morning. Today is a little delayed. For those who want to learn bulk RNAseq analysis, check out these two tutorials: How to preprocess GEO bulk RNAseq data with salmon https://divingintogeneticsandgenomics.com/post/how-to-preprocess-geo-bulk-rnaseq-data-with-salmon/ Downstream of bulk RNAseq: read in salmon output...

Hello Bioinformatics lovers, If you work on single-cell RNAseq data, do you know Seurat (in R) and scanpy (in python) had a discrepancy in calculating log2Fold change for marker genes per cluster? Read more details in this blog post: https://divingintogeneticsandgenomics.com/post/do-you-really-understand-log2fold-change-in-single-cell-rnaseq-data/ In this video, I show you how to use google gemini multi-modal to write math formula in Latex by feeding a screenshot to it: Other useful resources...

Hello Bioinformatics lovers, There are some hidden gems beyond the typical programming skills that have been instrumental in my journey. These are the often-overlooked yet crucial practices that have empowered me to tackle challenges and make sense of data in meaningful ways. Watch the full video here. Firstly, let’s talk about patience. It’s not as glamorous as diving straight into analysis, but taking the time for thorough quality control is invaluable. Before you get carried away,...