Identify differentially expressed gene markers for cell clusters in single-cell RNA-seq data.
npx skills add https://github.com/pwwang/immunopipe --skill clustermarkers
Please help me install this Agent Skill. Skill: clustermarkers Source: https://github.com/pwwang/immunopipe/tree/main/skills/clustermarkers Command: npx skills add https://github.com/pwwang/immunopipe --skill clustermarkers
Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function. Performs statistical testing between clusters, identifies cluster-defining genes, and automatically runs pathway enrichment analysis (via Enrichr) on significant markers. Generates publication-ready visualizations including volcano plots, dot plots, heatmaps, and enrichment plots.
Run cluster marker analysis on a SeuratClustering object to identify cluster-defining genes and generate enrichment visualizations.
High-intent search queries and answers about installing and using this skill.
To identify differentially expressed genes for clusters in Seurat single-cell RNA-seq data, use FindMarkers to statistically test between clusters and define cluster-specific genes.
Yes, you can automatically run pathway enrichment on Seurat cluster markers using Enrichr, which analyzes significant markers to reveal functional themes and generate enrichment plots.
Generating publication-ready visualizations for single-cell cluster markers involves creating volcano plots, dot plots, and heatmaps from Seurat FindMarkers results to interpret cluster identities.
You need to perform cluster marker identification after single-cell clustering to interpret cluster identities, annotate cell types, and drive downstream enrichment analyses.
Yes, cluster marker analysis supports T and B cell single-cell data, finding differentially expressed genes for clusters of T/B cells using Seurat's FindMarkers function.
Outputs from single-cell cluster marker and enrichment analysis include marker tables for reporting, pathway enrichment results, and publication-ready visuals like volcano plots and heatmaps.
anthropicsFilter low-quality cells from single-cell RNA-seq data using MAD-based QC.
ya-wayIdentify cluster-specific marker genes and annotate cell types in single-cell RNA-seq data.
KetomihineRun Seurat v5 single-cell RNA-seq analysis in R from .rds/.rdata inputs.
openscientist-ioIdentify differential gene expression patterns from RNA-seq and transcriptomics data.
