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The Modern R Stack for Production AI
Python isn't the only game in town anymore: R can interact with local and cloud LLM APIs, inspect and modify your local R environment and files…
Jun 2
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Stephen Turner
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The Modern R Stack for Production AI
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May 2025
Weekly Recap (May 2025, part 3)
Polars-bio, LiftOn, feature selection for scRNA-seq, STRkit for genotyping STRs with long reads, nf-core/detaxizer, Uncalled4, RegionScan, CREsted…
May 27
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Weekly Recap (May 2025, part 3)
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Writing a book with Quarto
Turn a collection of RMarkdown documents into a book in <1 hour using Quarto
May 19
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Stephen Turner
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Writing a book with Quarto
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Weekly Recap (May 2025, part 2)
Comprehensive evolutionary modeling of human gene function, an AI reasoning model for rare disease diagnosis, an AI agent for scRNA-seq data…
May 15
1
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Weekly Recap (May 2025, part 2)
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uv, part 3: Python in R with reticulate
Two demos using Python in R via reticulate+uv: (1) Hugging Face transformers for sentiment analysis, (2) pyBigWig to query a BigWig file and visualize…
May 6
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Stephen Turner
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uv, part 3: Python in R with reticulate
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Weekly Recap (May 2025, part 1)
Methods in genetic epidemiology, privacy-preserving methods for QTL and GWAS analysis, family-based GWAS, lots of Nextflow for PGS construction…
May 2
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Weekly Recap (May 2025, part 1)
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April 2025
Listen to papers, PDFs, and articles with ElevenReader
ElevenReader (free for iOS/Android) will read articles and PDFs in realistic voices. Example clips here with Burt Reynolds, Maya Angelou, and Richard…
Apr 25
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Stephen Turner
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Listen to papers, PDFs, and articles with ElevenReader
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Weekly Recap (April 2025, part 2)
Effector genes at GWAS hits, protein evolution, regulatory variant prediction, gene/genome duplication analysis, genomic foundation models, Nextflow…
Apr 24
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Stephen Turner
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Weekly Recap (April 2025, part 2)
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R 4.5.0 and Bioconductor 3.21
Faster package installation, import only the functions you want with use(), built-in Palmer penguins data, grep values shortcut, and lots of new…
Apr 17
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Stephen Turner
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R 4.5.0 and Bioconductor 3.21
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Weekly Recap (April 2025, part 1)
Evo2, genomic foundationless models, the ggalign R package, ancestral reconstruction for ancient DNA, biodiversity genomics reviews, structural…
Apr 11
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Weekly Recap (April 2025, part 1)
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Build a local RAG application with Open WebUI to chat with your Zotero library
Demonstration using Mistral and Nomic Embed with Ollama and Open WebUI
Apr 5
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Stephen Turner
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Build a local RAG application with Open WebUI to chat with your Zotero library
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March 2025
Weekly Recap (March 2025, part 2)
AI agents for biomedical reasoning, species tree inference, a spatial transcriptomics foundation model, biomedical research with LLMs, mapping cells…
Mar 28
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Weekly Recap (March 2025, part 2)
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