Zehua Zeng
Community@starlitnightly · CA94025
A student
Agent Skills by Zehua Zeng
Showing 50 vetted skills indexed across 3 GitHub repositories.
Starlitnightlyomicverse-reference-label-transfer
Transfer cell labels between AnnData objects using weighted kNN models.
Starlitnightlyomicverse-single-cell-cellphonedb-communication
Run CellPhoneDB permutation tests on AnnData and produce visualization-ready interaction objects.
Starlitnightlyomicverse-single-cell-scenic
Run SCENIC regulon inference on single-cell AnnData objects.
Starlitnightlyomicverse-single-cell-cnmf-program-discovery
Run consensus non-negative matrix factorization on single-cell AnnData to discover gene programs.
Starlitnightlyomicverse-cross-modal-celltype-transfer
Transfer cell-type labels between AnnData objects using weighted KNN.
Starlitnightlyomicverse-single-cell-cytotrace2
Predict developmental potency scores from single-cell AnnData matrices using pretrained CytoTRACE2.
Starlitnightlyomicverse-single-cell-preprocessing
Convert raw AnnData objects into preprocessed, clustered single-cell RNA-seq data.
Starlitnightlyomicverse-single-cell-annotation
Annotate clustered AnnData objects with cell-type labels using CellTypist, GPT-based, or SCSA backends.
Starlitnightlyomicverse-single-cell-batch-integration
Automate batch integration of preprocessed single-cell AnnData across multiple backends.
Starlitnightlyomicverse-single-cell-differential-expression
Compare conditions per cell type in AnnData with Wilcoxon, t-test, or memento backends.
Starlitnightlyomicverse-single-cell-rna-velocity
Automate single-cell RNA velocity analysis on AnnData objects with OmicVerse.
Starlitnightlyomicverse-single-cell-sctour-trajectory
Compute scTour pseudotime, latent embeddings, and vector-field outputs from raw-count AnnData.
Starlitnightlyomicverse-single-cell-clustering-backends
Compare Leiden, Louvain, GMM, and scICE clustering backends on AnnData embeddings.
Starlitnightlyomicverse-single-cell-differential-abundance
Run differential cell-type abundance analysis on single-cell AnnData between conditions.
Starlitnightlyomicverse-single-cell-lda-topic-clustering
Run LDA topic modeling on AnnData count data with a MIRA backend.
Starlitnightlyomicverse-single-cell-trajectory-inference
Infer trajectories and summarize lineages on cluster-ready AnnData objects.
Starlitnightlyomicverse-single-cell-kb-alignment
Build kb references and quantify scRNA-seq FASTQs into count matrices with OmicVerse alignment wrappers.
Starlitnightlybiocontext-knowledge-queries
Query 49 biomedical databases for gene annotation, pathways, literature, and drugs.
Starlitnightlyfastq-analysis-pipeline
Orchestrate RNA-seq analysis from FASTQ files to gene count matrices.
Starlitnightlydatasets-loading
Load curated bioinformatics datasets and generate configurable mock datasets.
Starlitnightlyscenic-gene-regulatory-network
Infer gene regulatory networks from single-cell RNA sequencing data.
Starlitnightlyfoundation-model-analysis
Generate cell embeddings and annotate single-cell data using 22 foundation models via omicverse's unified API.
Starlitnightlycellfate-pseudotime-gene-analysis
Identify lineage-specific fate genes along pseudotime trajectories in scRNA-seq data.
Starlitnightlydata-io-loading
Read and write omics data files in h5ad, 10x Genomics, Visium, Nanostring, and CSV formats.