bio-small-rna-seq-differential-mirna
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.
npx skills add BioTender-max/awesome-bio-agent-skills --skill differential-mirna --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, ggplot2 3.5+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Differential miRNA Expression **"Find differentially expressed miRNAs between my conditions"** → Perform statistical testing on miRNA count matrices to identify miRNAs with significant expression changes, accounting for small RNA-specific normalization considerations. - R: `DESeq2::DESeq()` or `edgeR::glmQLFTest()` on miRNA count data ## Load miRNA Count Data ```r library(DESeq2) # Load miRge3 or miRDeep2 counts counts <- read.csv('miR.Counts.csv', row.names = 1) # Create sample metadata coldata <- data.frame( sample = colnames(counts), condition = factor(c('control', 'control', 'treated', 'treated')), row.names = colnames(counts) ) ``` ## DESeq2 Analysis **Goal:** Identify miRNAs with significant expression changes between experimental conditions, accounting for
- Version Compatibility
- Load miRNA Count Data
- DESeq2 Analysis
- Apply Shrinkage for Effect Sizes
- Filter Significant miRNAs
- edgeR Alternative
- Visualization
- Heatmap of DE miRNAs
- Export Results
- Related Skills
What does the bio-small-rna-seq-differential-mirna skill do?
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill differential-mirna --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.