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RNA-seq comparison preparer

Give it sequencing output. Get counts ready to compare gene activity between groups, with replicate and setup checks.

RNA-seq comparison preparer is a free AI skill for the job "Research a topic properly". Give the instructions to an AI assistant that supports the required files and tools, then review its output.

Free · No account · MIT licence · Made by K-Dense · Level: advanced · Thinking: high

Made by K-Dense. See the original on GitHub; we copied it as it is, with its licence.

What it does

Sequencing output turned into a checked table of gene counts, ready to compare gene activity between groups. Mistakes in set-up are caught before they ruin the analysis. The skill takes FASTQ files or output from Salmon, STAR or featureCounts, and can set up the nf-core/rnaseq pipeline. It validates the sample list, checks you have real biological replicates, confirms strandedness and records which reference was used. Quality checks run before and after counting. It then assembles a counts matrix with the right sample and gene order and hands it to PyDESeq2. It needs Python with pandas and numpy, and often Nextflow with containers.

You give it

FASTQ files or quantification output
A sample sheet with groups
The reference genome or transcriptome used
Batch information (optional)
Python and, for raw reads, Nextflow set up

You get

A validated counts matrix
A matching sample metadata table
Quality and replicate checks
A record of settings and versions
A handoff ready for PyDESeq2

Use it when

You have raw reads and need a counts table.
You want to check your experiment has enough replicates before paying for compute.
Salmon output must become a matrix for DESeq2.
You are unsure about strandedness or reference settings.

How to use it

Add it to your AI once: download it and add the folder to Claude, ChatGPT or Codex as a skill.
Ask for the job in your own words. Your AI opens the skill when it fits.
It works best when your AI can run Python and command line tools.