Agent Skills by Shuotong Song
Showing 92 vetted skills indexed across 1 GitHub repositories.
ya-waybio-de-results
Extract, filter, annotate, and export DESeq2 and edgeR differential expression results.
ya-waysc-data-profiler
Profile raw 10x Genomics single-cell matrices to output QC distributions as JSON.
ya-waybio-pathway-enrichment-visualization
Generate publication-quality ggplot2 figures from GO, KEGG, and GSEA enrichment results.
ya-waybio-gene-regulatory-networks-multiomics-grn
Infer enhancer-driven gene regulatory networks from paired scRNA-seq and scATAC-seq data with SCENIC+.
ya-wayreactome-database
Identify enriched Reactome pathways from gene lists via REST APIs and reactome2py.
ya-waybio-single-cell-cell-annotation
Automate cell-type labeling for single-cell gene expression data using reference-based methods.
ya-waygene-database
Query NCBI Gene via E-utilities and Datasets API for gene metadata.
ya-waycytoclaw-reproducible-notebook
Generate a reproducible Jupyter notebook documenting the Cytoclaw analysis pipeline with nbformat.
ya-waybio-spatial-transcriptomics-spatial-visualization
Overlay gene expression and annotations on tissue sections using Squidpy and Scanpy.
ya-waybio-data-visualization-heatmaps-clustering
A data analysis tool that generates a clustered heatmap from a matrix of expression values, with optional row/column annotations and multiple output formats.
ya-waybio-single-cell-multimodal-integration
Integrate multi-modal single-cell RNA, protein, and ATAC data into unified representations.
ya-waybio-de-edger-basics
Identify differentially expressed genes from RNA-seq count data using edgeR.
ya-waysc-dynamic-clustering
Normalizes scRNA-seq data and clusters it with Leiden or Louvain into an annotated AnnData.
ya-waybio-pathway-reactome
Analyzes Reactome pathway enrichment for gene lists using enrichPathway and gsePathway.
ya-waybio-spatial-transcriptomics-spatial-statistics
Compute spatial statistics for spatial transcriptomics data with Squidpy and Scanpy.
ya-waybio-single-cell-trajectory-inference
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo.
ya-waybio-single-cell-doublet-detection
Detect and remove doublets in single-cell RNA-seq data using Scrublet, DoubletFinder, and scDblFinder.
ya-waybio-workflows-multiome-pipeline
Analyze joint scRNA-seq and scATAC-seq data with Seurat/Signac WNN integration.
ya-wayfeishu-sheets
Automate create, read, write, and append operations on Feishu Sheets via Python CLI.
ya-waybio-single-cell-preprocessing
Automate QC, filtering, and normalization for single-cell RNA-seq data with Seurat and Scanpy.
ya-waybio-data-visualization-multipanel-figures
Assemble individual plots into publication-ready multi-panel figures with shared legends.
ya-wayscrna-orchestrator
Coordinate end-to-end single-cell RNA-seq analysis from raw counts or 10x inputs.
ya-waybio-data-visualization-network-visualization
Visualize biological networks as static figures and interactive HTML using NetworkX and PyVis.
ya-waybio-data-visualization-volcano-customization
Generate publication-ready volcano plots from differential expression results.