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) Cookiecutter project templates, and (3) modern tools in the Python packaging ecosystem.

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.

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., tibble listcols). Use it instead of CSV. Many pros, few (no?) cons. Yesterday I wrote about base R vs. dplyr vs. duckdb for a simple summary analysis.

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 into memory. The duckplyr package wraps DuckDB's analytical query processing techniques in a dplyr-compatible API.

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

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 signals and forecasts.

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;DR I wrote an R package that summarizes recent bioRxiv preprints using a locally running LLM via Ollama+ollamar, and produces a summary HTML report from a parameterized RMarkdown template.

This is reposted from the original article:

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.

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.

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 lots of areas related to development in R, including the tidyverse, the RStudio IDE, Shiny, htmlwidgets, and authoring with RMarkdown.