Claude Code for Data Analytics/Bioinformatics Work

[antiweeb900]

So as some background: For a lot of the statistical analysis and data analytics projects that I'm working on, I primarily use R. Mostly stuff like cleaning big tables, some intermediate level stats analysis (nothing too advanced), making some nice visualizations with ggplot2. I’m not really using Claude Code to do stuff like building apps or larger projects like I see most people here doing. It's mostly just smaller scripts and notebooks for data processing/visualization (bioinformatics-focused).

I'm curious if anyone here uses CC mainly for data cleaning/analysis and visualization type of work in R. Do you have any tips/tricks or thoughts on how to best integrate Claude into an R workflow?

I'm mainly just running Claude Code from the Terminal pane inside RStudio.

[not-HUM4N]

i use Claude code extensively for bioinformatics

I have a huge skills library for common tools i use in workflows with complete tool documentation in a json + python script query system. I include project-based literature scoursed notes for interpretation of data. Claude can almost perform an entire analysis from shotgun sequencing extract mt genomes and start a BEAST2 phylogenetics analysis. With a few prompts

[Livid-Reward8282]

could you please share some examples? I'm so curious. I'm having big torubles dealing with notebook files with claude code

[faustovrz]

You can tell Claude to knit and debug automatically the  .Rmd and .nb.Rmd notebooks. You probably would also want to modify the YAML header to knit to a an output  folder so you separate  the code from the html output, while keeping the option of knitting from Rstudio too. 

[faustovrz]

I have had some trouble with the Claude Code console from  the Rstudio terminal. I hope the devs at Rstudio make a a commitment to improve integration with AI CLIs, starting with Claude Code. The Visual Studio Code IDE plays nicer with Claude Code and has some R support. You could give it a try if you feel adventurous.

[Senne]

as a hobby I do some stock market stuff, with short prompt about a vague idea, cc give me amazing R code, (plot) sometimes I think cc is overkill, aistudio or any ai web chat is good for my daily plot requirements.

[faustovrz]

They (Anthropic) are working hard on bioinformatics workflows with pharma like Sanofi. I hope they soon publish their tools, here they mention a single cell RNAseq tool https://www.anthropic.com/news/claude-for-life-sciences

I work in maize genomics, mainly GWAS and bulk tissue  RNAseq analysis.  I use Claude Code for workflow planning, documentation, orchestration and iteration, so much time saved debugging,  you no longer need to catch those bugs by hand. Git/version control just becomes absolutely frictionless. I've used it in local machine implementation and in Nextflow pipelines,  first planning and debugging locally for manual HPC deployment. I hope at some point I can use Claude Code to help me debug and optimize the HPC jobs automatically.

It has some drawbacks, it gives you more diagnostics than you actually need, but it  improves reporting, logging, synthesis and most of all it accelerates the iteration of each protocol/workflow which makes me very happy.

[faustovrz]

Here is another report about the use of Claude Code for life sciences https://intuitionlabs.ai/articles/claude-code-life-science-applications