bio-de-results
Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.
npx skills add BioTender-max/awesome-bio-agent-skills --skill de-results --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+ 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. # DE Results Extract, filter, and export differential expression results. ## Required Libraries ```r library(DESeq2) # or library(edgeR) library(dplyr) # For data manipulation ``` ## Extracting DESeq2 Results **Goal:** Retrieve DE statistics from a fitted DESeq2 model as a usable data frame. **Approach:** Call results() with optional shrinkage, then convert to a data frame with gene identifiers. ```r # Basic results res <- results(dds) # With specific alpha (adjusted p-value threshold) res <- results(dds, alpha = 0.05) # With log fold change shrinkage res <- lfcShrink(dds, coef = 'condition_treated_vs_control', type = 'apeglm') # Convert to data frame res_df <- as.data.frame(res) res_df$gene <- rownames(res_df) ``` ## Extracting edgeR Results **Goal:** Retrieve DE statistics from a fitted edge
- Version Compatibility
- Required Libraries
- Extracting DESeq2 Results
- Extracting edgeR Results
- Filtering Significant Genes
- By Adjusted P-value
- By Fold Change
- Combined Filters
- Ordering Results
- Summary Statistics
- Adding Gene Annotations
- From Bioconductor Annotation Package
- From BioMart
- From Custom File
What does the bio-de-results skill do?
Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill de-results --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.