Bio Differential Expression Batch Correction
CheckedThis skill automatically corrects for batch effects in gene expression data, ensuring more accurate downstream analysis and reliable results.
Install on your platform
Showing Claude Code. One command installs this skill into any of the agents below.
- 1
Run this in your project
terminal$ npx skills add gptomics/bioskills --skill bio-differential-expression-batch-correction --full-depth -a claude-code Uses the open-source
skillsCLI and needs Node.js. Add-gto install it for your user instead of this project.
What we know about this skill
Publisher
gptomics
Taken from the source listing. We haven't verified who controls this account.
Install target
Live repository
Not pinned. Installing fetches whatever the repository holds at the time you run the command.
Automated safety checks
This skill passed all 6 checks. We read its files at one commit and looked for the things that make a skill dangerous to run — not for whether it works.
Declares what it does: passed
SKILL.md parses and declares a name and a description.
SKILL.md exists, its frontmatter parses, and it declares a name and a description.
No undeclared network calls: passed
Makes no network calls.
Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.
No obfuscated payloads: passed
No encoded or obfuscated payloads.
No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.
No credential access: passed
Reads no keys, tokens, keychains or credential files.
Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.
No pipe-to-shell installers: passed
No pipe-to-shell or download-and-run installers.
No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.
Pinned to a commit: passed
Scanned gptomics/bioskills at d91ed3d563.
The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.
- Commit
- d91ed3d563
- Scanned
- 3 files, 465 lines
About this skill
What it does
This skill performs batch correction on RNA sequencing (RNA-seq) data for differential expression analysis. It addresses technical variation between samples, allowing for more accurate identification of genes with altered expression levels across different conditions or groups. The skill aims to normalize and harmonize datasets that have been processed using varying experimental protocols or platforms.
When to use it
- Comparing gene expression profiles from experiments performed in different labs.
- Integrating data from multiple sequencing runs conducted at various times.
- Analyzing RNA-seq data where samples were prepared using different methods.
- Correcting for confounding factors introduced by batch effects during library preparation or sequencing.
Key capabilities
- Batch effect removal
- RNA-seq data normalization
- Differential expression analysis preparation
- Harmonization of datasets from varying experimental protocols
Example prompts
- "Apply batch correction to my RNA-seq count matrix."
- "Normalize and correct for batch effects in this dataset before differential expression testing."
- “Prepare the following RNA-seq data for downstream differential expression analysis, accounting for potential batch variations.”
Tips & gotchas
- Requires a properly formatted RNA-seq count matrix as input.
- The effectiveness of batch correction depends on the nature and magnitude of the batch effects present in the data.