Heatmap in ggplot2 yunuuuu.github.io/ggalign/ind... I always use complexheatmap, but this seems to be a good alternative if you want to stay within the ggplot

chatomics! Uncover the Secrets of Unix Systems with the Path Variable! Watch Now: www.youtube.com/watch?v=nve...

Survival analysis is a critical skill for bioinformaticians. But be careful about interpretation 🧵👇 patients with high expression of gene A have better survival. Should you activate it?

Best Practice for R :: Cheat Sheet #rstats github.com/wurli/r-bes...

Depending on your data type, use the right plot to tell the story. A nice interactive app to determine what plots you need www.data-to-viz.com/

1/ Public datasets feel like a goldmine. But look closer—there are landmines hidden inside. Especially for single-cell RNA-seq. A thread 🧵

1/ Everyone wants to slap “AI” on their title. I told a conference organizer I’m not an AI expert (yet). She looked shocked. Here’s why.

1/ The first time I saw a red error message, I thought I broke everything. Turns out—it was just the computer trying to help me.

chatomics! How to Align multiple ggplot2 plots by axis #rstats divingintogeneticsandgenomics.com/post/align-...

Nature Protocols: High-resolution single-cell sequencing of trans-spliced mRNA www.nature.com/articles/s4...

1/ How to quantify a transgene (e.g., TdTomato, GFP) in scRNAseq data? You need to add the transgene to the reference. See my post divingintogeneticsandgenomics.com/post/cellra... However, it is not always working 👇

1/ One of the biggest hidden killer in bioinformatics? Not a bug. Not a crash. It’s the 0-based vs 1-based coordinate trap. A thread 🧵

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data www.nature.com/articles/s4...

A Bioinformatician's UNIX Toolbox I know I am still old-school :) lh3lh3.users.sourceforge.net/biounix.shtml

1/ Why I sometimes ignore Nature Methods papers when picking bioinformatics tools. A practical guide to choosing tools that actually work.

Scalable and unsupervised discovery from raw sequencing reads using SPLASH2 www.nature.com/articles/s4...

1/ I stopped trying to keep up with every new *Seq method— and my career got better. Here’s why that mindset shift matters.

You’re drowning in bioinformatics tools. You think you need the “best” one. You don’t. You just need to start.

Integrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets www.nature.com/articles/s4...

Think you’ll remember every step of your bioinformatics project 3 months from now? You won’t. And it will cost you.

1/ I’ve reviewed hundreds of bioinformatics GitHub repos in my career. Here’s the brutal truth: most tool documentation fails the people it’s meant to help. And it’s not because the algorithms are bad.

Tumor transcriptional state predicts survival in immune-checkpoint-blockade-treated glioblastoma www.nature.com/articles/s4...

1 / “Expert in bioinformatics?” Yes and no. Here’s why that’s both true and false—and why it matters for your career.

Bioinformatics doesn’t break you with code. It breaks you with the invisible details in data. That’s where most people get lost. 🧵

Two tools for plotting genomics data: figeno: Tool for making genomics figures in #python. github.com/CompEpigen/... Plotting Multi-omic Data with plotgardener in #rstats phanstiellab.github.io/plotgardene...

Run the same agentic bioinformatics analysis five times. You will get five different answers. Even on a well-defined task. This is not a bug you can patch out. It is the nature of LLMs.

Struggling to “get” bioinformatics? You’re not alone. The truth is: real understanding doesn’t happen the first time. It happens on the fifth. Or the tenth. Here’s my journey of relearning PCA, stats, and bioinformatics—and why repetition is the secret weapon. 🧵

1/ A boy who ate tree bark to survive grew up to carry a whole country on his back. I spent two hours of commute with Chung Ju-yung's story today, and I can't stop thinking about one thing: he refused to call anything a failure.

MIND: multimodal integration with neighbourhood-aware distributions www.nature.com/articles/s4...

1/ So do you still need the fundamentals now that AI writes the code? More than before. Your job shifted from typing commands to judging whether the results hold up, and that judgment runs on understanding the methods underneath.

If you’re waiting for perfect bioinformatics data, you’ll never publish. ChIP-seq taught me this the hard way

solid foundation in statistics is even more important in the age of AI. This interactive app explaining statistic concepts is great seeing-theory.brown.edu/index.html

1/ Want to reorder bars in ggplot2? The tidy way is tidyplot::sort_x_axis_labels(). But let’s pull back the curtain and see what’s really happening. 🧵

I keep getting asked the same question: should I use nextflow/Snakemake or a Claude Code agent for my analysis? Wrong question. They are tools for different problems.

Do you really understand p-values? The p-value histogram can reveal a LOT about your data. Let's break it down using real examples.👇

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility www.nature.com/articles/s4...

Everyone talks about KNN like it’s a simple algorithm. But in practice, especially in single-cell RNA-seq—it’s art, not science.

1/ AI won’t save your bioinformatics pipeline if your metadata is a mess. You can’t model what you don’t understand. Let’s talk about the real bottleneck in public data: metadata. 🧵

scPair: Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases www.nature.com/articles/s4...

1/ Many genomics mistakes are hard to catch in the code. They’re in the data you never looked at. Genome browsers can change that. Here’s how.

My next newsletter "Will AI replace bioinformaticians?" is coming at 9:30 am. Subscribe to get it and stay in the loop on everything I'm creating. divingintogeneticsandgenomics.kit.com/profile

Enjoy the journey. daily-quote-app-mu.vercel.app/

“I think I’m greedy, but I’m not greedy for money—I think that can be a burden—I’m greedy for an exciting life.”​ — David Hockney

Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery www.nature.com/articles/s4...

1/ Bioinformatics is NOT just statistics. The p-value is small, but is it biologically meaningful? Let’s talk. 🧵

1/ In bioinformatics, your analysis is only as strong as the workflow behind it. That’s why workflow language matters. 🧵 Let’s talk about workflow languages—and why you need one.

Multi-omic characterization of nasopharyngeal carcinoma delineates the subtype-specific landscape of response to induction chemotherapy www.nature.com/articles/s4...

1/ Two patients. Same drug. Same total dose. One gets better. One gets worse. Why? Because dose and schedule can make or break a drug. Let's talk about the unsung science of getting this right. 🧵

1/ Why is bioinformatics so complicated? Because biology is messy, layered, and full of exceptions. Let me show you with one simple question.

barbieQ: an R software package for analysing barcode count data from clonal tracking experiments academic.oup.com/bioinformat...