bio-de-deseq2-basics
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-de-deseq2-basics --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+, Salmon 1.10+, edgeR 4.0+, 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. # DESeq2 Basics Differential expression analysis using DESeq2 for RNA-seq count data. ## Required Libraries ```r library(DESeq2) library(apeglm) # For lfcShrink with type='apeglm' ``` ## Installation ```r if (!require('BiocManager', quietly = TRUE)) install.packages('BiocManager') BiocManager::install('DESeq2') BiocManager::install('apeglm') ``` ## Creating DESeqDataSet **Goal:** Construct a DESeqDataSet object from various input formats for DE analysis. **Approach:** Wrap count data and sample metadata into the DESeq2 container, specifying the experimental design formula. **"Load my RNA-seq counts into DESeq2"** → Create a DESeqDataSet from a count matrix, SummarizedExperiment, or tximport object with sample metadata and a design formula. ### From Count Matrix ```r
- Version Compatibility
- Required Libraries
- Installation
- Creating DESeqDataSet
- From Count Matrix
- From SummarizedExperiment
- From tximport (Salmon/Kallisto)
- Standard DESeq2 Workflow
- Design Formulas
- Specifying Contrasts
- Log Fold Change Shrinkage
- Setting Significance Thresholds
- Accessing DESeq2 Results
- Result Columns
What does the bio-de-deseq2-basics skill do?
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-de-deseq2-basics --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.