Wei He
Community@mdhewei · Houston, TX
Ph.D. major in Bioinformatics, senior computational biologist working on CRISPR, Alphafold, NGS, Epigenetics ,cancer biology and more.
Agent Skills by Wei He
Showing 48 vetted skills indexed across 1 GitHub repositories.
MDheweibioinformatics-plot-generator
Route bioinformatics plot requests to specialized sub-skills for figure generation.
MDheweigeo-download-data
Fetch GEO datasets and parse series_matrix into expression matrices and metadata.
MDheweitcga-download-data
Download TCGA genomic datasets from the GDC Data Portal with streaming and MD5 verification.
MDheweigtex-download-data
Download GTEx expression data matrices from the GTEx Portal API or static files.
MDheweidepmap-download-data
Download selective DepMap datasets from specified releases with caching and manifests.
MDheweipaper-digest-single
Generate a structured markdown digest from a PubMed ID, DOI, arXiv ID, or local PDF.
MDheweipubmed-search
Search PubMed, rank results, and export TSV and markdown reports.
MDheweibioinformatics_big_papers_weekly_report
Retrieve recent bioinformatics papers and generate ranked TSV and PDF reports.
MDheweipreprint-tracker
Query bioRxiv and medRxiv APIs to compile preprint metadata, abstracts, and author lists.
MDheweidepmap-analysis-for-gene
Analyzes a single gene across DepMap cancer cell lines using multi-module methods including expression, mutation, copy_number, essentiality, coexpression, and coessentiality, producing summaries and plots.
MDheweicox-survival-analysis
Analyzes time-to-onset data with Cox proportional-hazards models and generates survival curves and related metrics from RCTs or cohort studies.
MDheweicoexpression-for-gene
Identify genes co-expressed with a query gene across TCGA and GTEx datasets.
MDheweidrug-sensitivity-for-gene
Correlate gene expression or dependency vectors with drug sensitivity across cancer cell lines.
MDheweitcga-expression-for-gene
Query live GDC data to plot single-gene expression across TCGA cancer cohorts.
MDheweimutation-analysis-for-gene
Summarize gene mutations from TCGA cohorts via cBioPortal or local MAF files.
MDheweinormal-tissue-expression-for-gene
Resolve normal tissue expression for a single gene using GTEx data.
MDheweitcga-survival-for-gene
Perform Kaplan-Meier analysis linking gene expression to TCGA survival outcomes via the GDC API.
MDheweiProtein Structure Alignment
Align two protein structures by Cα superimposition to compute global RMSD and per-residue deviations.
MDheweiprotein-structure-visualizer
Visualize and analyze protein structures from PDB IDs, AlphaFold entries, or local files.
MDheweiprotein-structure-for-gene
Resolve gene symbols to UniProt accessions and render domain maps.
MDheweiprotein-sequence-analysis
Compute physicochemical properties, motifs, and domains from protein sequences.
MDheweiclustering-analysis
Partition omics samples or features into clusters based on expression similarity.
MDheweidimensionality-reduction
Reduce high-dimensional omics matrices to 2D/3D projections with PCA, UMAP, and t-SNE.
MDheweiomics-ml-classifier
Train supervised machine learning classifiers on omics data with cross-validated metrics.