Agent Skills by Panwen Wang
Showing 33 vetted skills indexed across 1 GitHub repositories.
pwwangseuratsubclustering
Re-cluster selected cell subsets within a Seurat object using PCA, UMAP, and clustering workflows.
pwwangtopexpressinggenesofallcells
Identify top expressing genes per cluster and perform pathway enrichment.
pwwangmetabolicpathwayheterogeneity
Compute NES scores for metabolic pathways across scRNA-seq cell groups.
pwwangclonalstats
Compute clonality statistics and diversity visualizations for TCR/BCR repertoires.
pwwangmetabolicpathwayactivity
Calculate metabolic pathway activity scores across cell groups in Seurat objects.
pwwangseuratclusteringofallcells
Cluster all cells at coarse resolution using Seurat FindClusters.
pwwangtessa
Analyzes paired TCR and RNA data to identify cell states via Bayesian inference.
pwwangmetabolicinput
Route Seurat objects to downstream metabolic analysis steps.
pwwangscrepcombiningexpression
Integrate TCR/BCR repertoires with scRNA-seq data to enrich Seurat metadata with clonotype information.
pwwangseuratpreparing
Load, preprocess, and integrate multi-sample scRNA-seq data into a Seurat object.
pwwangtopexpressinggenes
Identify top expressed genes per cluster and perform pathway enrichment analysis on scRNA-seq data.
pwwangscrnametaboliclandscape
Coordinate metabolic pathway analysis workflows for scRNA-seq data with Seurat inputs.
pwwangscreploading
Load scTCR-seq or scBCR-seq data into a scRepertoire-compatible object.
pwwangcdr3clustering
Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR.
pwwangimmunopipe-config
Generate end-to-end immunopipe TOML configurations for RNA and TCR/BCR analyses.
pwwangsampleinfo
Ingests CSV/TSV sample metadata, performs statistical analyses, and generates visualization reports for single-cell RNA-seq pipelines.
pwwangloadingrnafromseurat
Load Seurat RDS or qs/qs2 objects into the immunopipe pipeline.
pwwangpseudobulkdeg
Aggregate single-cell counts into pseudo-bulk samples and test differential expression with DESeq2 or edgeR.
pwwangtorbcellselection
Separate T or B cells from mixed scRNA-seq data using clonotype percentages, marker genes, or k-means clustering.
pwwangscfgsea
Rank genes by differential expression to identify enriched pathways in single-cell data.
pwwangcellcellcommunication
Infer ligand-receptor interactions from single-cell RNA-seq data using LIANA+.
pwwangclustermarkersofallcells
Identify marker genes for all cell clusters before T/B cell selection.
pwwangmetabolicexpimputation
Impute dropout values in scRNA-seq expression matrices using ALRA, scImpute, or MAGIC.
pwwangmodulescorecalculator
Calculate per-cell module scores for Seurat single-cell data.