Stephen Turner | R-bloggers

Repost: Bluesky conversation analysis with local and frontier LLMs with R/Tidyverse

December 30, 2024 | Stephen Turner

Reposted from the original at https://blog.stephenturner.us/p/bluesky-analysis-claude-llama-tidyverse.Summary, translation, and sentiment analysis of Bluesky posts on a topic using atrrr, tidyverse/ellmer, and mlverse/mall with Claude and ot...

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Use an LLM to translate help documentation on-the-fly

December 16, 2024 | Stephen Turner

Reposted from Paired Ends at https://blog.stephenturner.us/p/llm-translate-documentation.---The lang package overrides the ? and help() functions in your R session. The translated help page will appear in the help pane in RStudio or Positron. It c...

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Turn a GitHub repo into a single text file for LLM-friendly input (repost)

December 9, 2024 | Stephen Turner

Reposted from the original at https://blog.stephenturner.us/p/github-repo-to-text-for-llm-input.--- If you use ChatGPT, Claude, or even some local model through Ollama or HuggingFace Assistants, you’ll know that the chat interf... [Read more...]

Tech I’m thankful for (repost)

November 25, 2024 | Stephen Turner

Reposted from https://blog.stephenturner.us/p/tech-im-thankful-for-2024Data science and bioinformatics tech I'm thankful for in 2024: tidyverse, RStudio, Positron, Bluesky, blogs, Quarto, bioRxiv, LLMs for code, Ollama, Seqera Containers, St... [Read more...]

Expand your Bluesky network with R (repost)

November 20, 2024 | Stephen Turner

This is reposted from the original at https://blog.stephenturner.us/p/expand-your-bluesky-network-with-r.---I’m encouraging everyone I know online to join the scientific community on Bluesky.Bluesky for ScienceStephen Turner·Nov 16Read full ...

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Build a Python CLI with Click+Cookiecutter (repost)

November 10, 2024 | Stephen Turner

Reposted from the original at https://blog.stephenturner.us/p/python-cli-click-cookiecutter. ---In the spirit of Learning in Public, I wanted an excuse to explore (1) click for creating command line interfaces, (2) Cookiec...

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Python for R users (repost)

October 22, 2024 | Stephen Turner

This is reposted from the original at https://blog.stephenturner.us/p/python-for-r-users.---A Google search for “R vs Python” returns thousands of hits across sites like Reddit, IBM, Datacamp, Coursera, Kaggle, and many others. A quick Googl...

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Use nanoparquet instead of readr/CSV

October 8, 2024 | Stephen Turner

This is reposted from the original at https://blog.stephenturner.us/p/use-nanoparquet-instead-of-readr-csv.Parquet is interoperable between Python and R, fast to read+write, works well with databases, and stores complex data types (e.g., tib...

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DuckDB vs dplyr vs base R

October 8, 2024 | Stephen Turner

Reposted from https://blog.stephenturner.us/p/duckdb-vs-dplyr-vs-base-r.TL;DR: For a very simple analysis (means by group on 100M rows), duckdb was 125x faster than base R, and 28x faster than readr+dplyr, without having to read data from disk int...

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Create a free Llama 3.1 405B-powered chatbot on any GitHub repo in 1 minute (cross-posted from Paired Ends)

September 11, 2024 | Stephen Turner

This blog has moved. This is reposted from Paired Ends:https://blog.stephenturner.us/p/create-a-free-llama-405b-llm-chatbot-github-repo-huggingfaceLlama 3.1 405B is the first open-source LLM on par with frontier models GPT-4o and Claude 3.5 Sonnet...

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PLANES: Plausibility Analysis of Epidemiological Signals

September 3, 2024 | Stephen Turner

This blog has moved. This is reposted from Paired Ends:https://blog.stephenturner.us/p/planes-plausibility-analysis-of-epidemiological-signals-rplanes-r-package PLANES provides a set of methods for evaluating the plausibility of epidemiological signal... [Read more...]

biorecap: an R package for summarizing bioRxiv preprints with a local LLM

August 24, 2024 | Stephen Turner

This is re-posted from my newsletter, where I'll be posting from now on:https://blog.stephenturner.us/p/biorecap-r-package-for-summarizing-biorxiv-preprints-local-llm---TL;DRI wrote an R package that summarizes recent bioRxiv preprints using a locally ...

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Use R to prompt a local LLM with ollamar

August 14, 2024 | Stephen Turner

This is reposted from the original article: https://blog.stephenturner.us/p/use-r-to-prompt-a-local-llm-withUse R to prompt a local LLM with ollamar: Using R to prompt llama3.1:70b running on my laptop with Ollama + ollamar to tell me what's inter...

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Moving to blog.stephenturner.us (Paired Ends)

July 30, 2024 | Stephen Turner

My new blog/newsletter ("Paired Ends") is now at blog.stephenturner.us. I'll be posting semi-regular updates and literature highlights in bioinformatics, computational biology, and data science, along with the occasional post on programming. Head ... [Read more...]

Staying Current in Bioinformatics & Genomics: 2017 Edition

February 1, 2017 | Stephen Turner

A while back I wrote this post about how I stay current in bioinformatics & genomics. That was nearly five years ago. A lot has changed since then. A few links are dead. Some of the blogs or Twitter accounts I mentioned have shifted focus or haven?... [Read more...]

RStudio Conference 2017 Recap

January 14, 2017 | Stephen Turner

The first ever RStudio conference was held January 11-14, 2017 in Orlando, FL. For anyone else like me who spends hours each working day staring into an RStudio session, the conference was truly excellent. The speaker lineup was diverse and covered lot... [Read more...]

Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

June 1, 2016 | Stephen Turner

How many reads do I need? What's my sequencing depth? These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what's the coverage depth given a set amount of sequenci...

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Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

June 1, 2016 | Stephen Turner

How many reads do I need? What's my sequencing depth? These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what's the coverage depth given a set amount of sequenci...

[Read more...]

Shiny Developer Conference 2016 Recap

February 5, 2016 | Stephen Turner

This is a guest post from VP Nagraj, a data scientist embedded within UVA’s Health Sciences Library, who runs our Data Analysis Support Hub (DASH) service.Last weekend I was fortunate enough to be able to participate in the first ever Shiny Developer Conference hosted by RStudio at Stanford ... [Read more...]

Shiny Developer Conference 2016 Recap

February 5, 2016 | Stephen Turner

This is a guest post from VP Nagraj, a data scientist embedded within UVA’s Health Sciences Library, who runs our Data Analysis Support Hub (DASH) service.Last weekend I was fortunate enough to be able to participate in the first ever Shiny Develope... [Read more...]

R-bloggers

R news and tutorials contributed by hundreds of R bloggers

Articles by Stephen Turner

Repost: Bluesky conversation analysis with local and frontier LLMs with R/Tidyverse

Use an LLM to translate help documentation on-the-fly

Turn a GitHub repo into a single text file for LLM-friendly input (repost)

Tech I’m thankful for (repost)

Expand your Bluesky network with R (repost)

Build a Python CLI with Click+Cookiecutter (repost)

Python for R users (repost)

Use nanoparquet instead of readr/CSV

DuckDB vs dplyr vs base R

Create a free Llama 3.1 405B-powered chatbot on any GitHub repo in 1 minute (cross-posted from Paired Ends)

PLANES: Plausibility Analysis of Epidemiological Signals

biorecap: an R package for summarizing bioRxiv preprints with a local LLM

Use R to prompt a local LLM with ollamar

Moving to blog.stephenturner.us (Paired Ends)

Staying Current in Bioinformatics & Genomics: 2017 Edition

RStudio Conference 2017 Recap

Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

Shiny Developer Conference 2016 Recap

Shiny Developer Conference 2016 Recap