1/Need to replace a pattern, but only in column 5? Don't touch the rest of the file. Don't reach for Excel. Here’s how real data wranglers do it.
Ming Tommy Tang
@tommytang.bsky.social
Director of bioinformatics at AstraZeneca. subscribe to my youtube channel @chatomics. On my way to helping 1 million people learn bioinformatics. Educator, Biotech, single cell. Also talks about leadership. tommytang.bio.link
🧵 You just got your hands on early clinical trial RNA-seq data. Excited? You should also be cautious. Here's why. 👇
Inference of secreted protein signaling activities in intercellular communication www.nature.com/articles/s4...
You have 50 files. Same header. You want to merge them. Here’s how to do it without going insane. 🧵 👇
Bioinformatics is hard before you even write a single line of code. Here's why. 1/ You haven’t started your DNA-seq analysis. You haven’t aligned a read. And yet you’ve already hit a wall. Which human genome to use?
We were in the pool at the gym, my kids splashing around, when another family walked in — and their little girl happened to be named Anna too.
Agentic genomics: From pipeline automation to autonomous validation www.cell.com/cell-genomi... The variant calling steps should be just automated with workflow languages, the variant intepretation part is what I see agents can do better a job (e.g, reading papers)
Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data www.nature.com/articles/s4...
1/ Bioinformatics isn't just code. It’s intuition. You run the stats, but you feel when something’s wrong. That feeling is a clue.
Ultra-fast and customizable Python charts. If you have a lot of points, try it. I can think of usage for single-cell visualization. reflex.dev/docs/xy/
Good tutorial: Removing tumour purity, library size and batch effects from the TCGA breast cancer RNA-seq data using RUV-III-PRPS https://htmlpreview.github.io/?https://github.com/RMolania/TCGA_PanCancer_UnwantedVariation/blob/master/Vigettes/TCGA_BRCA_RNAseq_Vignette.html
Your data is lying to you. Here’s how technical artifacts distort biology—and how to see the truth. 👇 1/ Beautiful t-SNE? Shiny heatmap? Look closer. Technical artifacts can fake whole cell types. Here’s where the ghosts hide.
I just published a newsletter: The plotting skill no package gives you divingintogeneticsandgenomics.kit.com/posts/the-p... subscribe to get all those bioinformatics tips for FREE!
A scientific plotting library in Rust. 60 plot types, SVG output, optional PNG/PDF backends, and a CLI binary that renders plots directly from the shell — including in the terminal itself. github.com/Psy-Fer/kuva
1/You know the feeling. You open a CSV or log file in the terminal— and it’s chaos. Wrapped lines. Misaligned columns. Impossible to read. Here’s how to turn that mess into clarity:
1/ No one tells you this: Coding isn’t about memorizing syntax. It’s about frustration, failure, and trying again anyway
Last day of daycare for my four-year-old. She switches to a new place in September.
Fix your data before you implement AI. We all know this: garbage in, garbage out. How many of us are actually doing it? It takes money and resources, but that's the dirty work no one wants to do. AI won't fix your dirty data.
scCustomize is an R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R. samuel-marsh.github.io/scCustomize/
An extremely fast R package manager, written in Rust. The R equivalent of uv for Python. · GitHub github.com/nbafrank/uvr
8 Resources to study Transcription factor binding, enhancers and histone modification distribution 1. ENCODE www.encodeproject.org/
SCpubr provides a streamlined way of generating publication ready plots for known Single-Cell visualizations github.com/enblacar/SC...
Almost every fusion transcript people report in plants is not real. A new Genome Biology paper looked at rice with long-read RNA-seq and found the vast majority are technical artifacts. Not biology. Not novel. Just noise your pipeline confidently labels as a fusion.
Rainy day. I drove to the airport to pick up my in-laws, flying in from China. My three kids hadn't slept — too excited the night before.
"Here we map cis-expression quantitative trait loci (eQTLs) across 2.2 million single cells using intestinal biopsies and blood from 421 individuals, including 125 with inflammatory bowel disease (IBD)." www.nature.com/articles/s4...
1/ If you're doing bioinformatics without Git, you're gambling with your research. Here are 6 Git commands every bioinformatician must know 🧵
After-dinner walk. My four-year-old is on her tricycle. She can't ride a bike yet — honestly, even pedaling three wheels is a struggle for her.
Pioneer transcription factors direct tissue-specific cohesin chromatin entry and three-dimensional genome organization www.nature.com/articles/s4...
