bio-workflows-multiome-pipeline
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.
npx skills add majiayu000/claude-skill-registry --skill multiome-pipeline-gptomics-bioskills-2 --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.
# Multiome Pipeline Complete workflow for 10X Multiome (joint scRNA + scATAC) analysis using Seurat and Signac. ## Workflow Overview ``` 10X Multiome data | v [1. Load Data] ---------> Read RNA + ATAC | v [2. RNA Processing] ----> Standard scRNA workflow | v [3. ATAC Processing] ---> Peak calling, LSI | v [4. WNN Integration] ---> Weighted nearest neighbors | v [5. Joint Analysis] ----> Clustering, markers | v [6. Linked Features] ---> Gene-peak links | v Integrated multiome object ``` ## Step 1: Load Multiome Data ```r library(Seurat) library(Signac) library(EnsDb.Hsapiens.v86) library(ggplot2) # Load RNA rna_counts <- Read10X_h5('filtered_feature_bc_matrix.h5') # For multiome, this returns a list with 'Gene Expression' and 'Peaks' # Create Seurat object with RNA seurat_obj <- CreateSeuratObject( counts = rna_counts$`Gene Expression`, assay = 'RNA' ) # Load ATAC atac_counts <- rna_counts$Peaks # Or from fragments file frags <- CreateFragmentObject('atac_fragments.tsv.gz', cells = colnames(seurat_obj)) # Create ChromatinAssay atac_assay <- CreateChromatinAssay( counts = atac_counts, sep = c(':', '-'), fragments = frags, annotation = GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86) )
- Workflow Overview
- Step 1: Load Multiome Data
- Step 2: RNA Quality Control and Processing
- Step 3: ATAC Quality Control and Processing
- Step 4: Weighted Nearest Neighbors (WNN)
- Step 5: Visualization and Markers
- Step 6: Gene-Peak Linkage
- Complete Workflow Script
- Related Skills
What does the bio-workflows-multiome-pipeline skill do?
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill multiome-pipeline-gptomics-bioskills-2 --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 majiayu000/claude-skill-registry, a repository with 534 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.