Retrieval-Augmented Generation
Back in February I learned about Open WebUI and have been wanting to test it out with Retrieval-Augmented Generation (RAG). I'll follow the tutorial available on Open WebUI's site. The goal of RAG ...
Dorado v1.0.0 and the v5.2.0 basecalling models
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Oxford Nanopore Should Spin Out Protein Sequencing
I've toyed with writing something on these lines for a long time but never quite pulled the trigger. But the more I think about it, the more imperative my logic feels for spinning off the nascen...
One tip per day
I have been adding one tip per day to my daily tips GitHub repo for the past month. It's a simple setup: I manually add tips to a YAML file I use a Python script to convert YAML to Markdown A helpe...
Multi-sample Integrative Analysis of Spatial Transcriptomics Data using Sketching and Harmony in Seurat
I often write up code tutorials as a way for me to take notes on what I’ve been learning. But they also serve a secondary purpose as training material for students in my lab. In particular, they provi...
Short RNA-seq read alignment with minimap2
TL;DR: the new preset splice:sr in minimap2 can align short RNA-seq reads.
It is similar to STAR in resource ...
FASTQ assemblies with Dorado polish
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Medaka vs Dorado polish
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Announcing: the chill-filter Web site - DNA sample composition at a glance!
what's in my sample, dude?
...A first look at CycloneSEQ data
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