zongtingwei

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for sequencing read QC, trimming, contamination screening, and pre-alignment cleanup.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for packaging analysis outputs into reproducible reports, clean tables, and publication-ready figure exports.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for foundational sequence parsing, conversion, compression handling, and interval-aware file validation.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for orchestrating reproducible omics pipelines with workflow engines and clear execution provenance.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

End-to-end EHR predictive modeling pipeline with PyHealth, covering dataset loading, task definition, model training, evaluation, calibration, and clinical interpretation.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for RNA modification analysis such as m6A peak calling, differential modification, and transcript-level visualization.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for Hi-C and related 3D genomics analyses including compartments, loops, TADs, differential contacts, and visualization.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for methylation alignment or calling, DMR analysis, methylation QC, and locus-level interpretation.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for orthology, synteny, ancestral reconstruction, and evolutionary comparison across genomes.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for nanopore or PacBio long-read QC, alignment, polishing, methylation-aware analysis, and structural variant discovery.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for haplotype phasing, genotype imputation, reference-panel matching, and imputation QC.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for small-variant and structural-variant discovery, filtering, annotation, and interpretation from sequencing data.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for amplicon microbiome analysis including denoising, taxonomy assignment, diversity analysis, and differential abundance.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for outbreak-style pathogen genomics, surveillance, lineage assignment, and transmission-oriented comparative analysis.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for multiple sequence alignment, tree inference, annotated tree visualization, and distance-based evolutionary comparison.

zongtingwei/Bioclaw_Skills_Hub

Skill Claude CodeCodex

Workflow for fine-mapping, colocalization, mediation, pleiotropy analysis, and Mendelian randomization.