| 01-01 | DESeq2 Differential Expression | Bulk Transcriptomics | DESeq2, size factor, Wald / LRT, apeglm |
| 01-02 | DE — Auto Method Selection | Bulk Transcriptomics | DESeq2, edgeR QL, limma-voom |
| 01-03 | Functional Enrichment | Bulk Transcriptomics | clusterProfiler, GSEA, ORA, MSigDB |
| 01-04 | Omics Clustering | Bulk Transcriptomics | hierarchical, k-means, HDBSCAN, GMM |
| 01-05 | Co-expression Network | Bulk Transcriptomics | WGCNA, module detection, hub genes |
| 02-01 | Scanpy Core Analysis | Single-cell & Spatial | Scanpy, CellBender, Scrublet, scVI / Harmony, Leiden |
| 02-02 | Seurat Core Analysis | Single-cell & Spatial | Seurat v5, SoupX, DoubletFinder, SCTransform, Harmony |
| 02-03 | Trajectory & Pseudotime | Single-cell & Spatial | PAGA, diffusion pseudotime, scVelo, CellRank |
| 02-04 | Cell–Cell Communication | Single-cell & Spatial | CellChat v2, ligand-receptor, chord / bubble plots |
| 02-05 | Regulatory Network (pySCENIC) | Single-cell & Spatial | GRNBoost2, cisTarget, AUCell |
| 02-06 | Spatial Transcriptomics | Single-cell & Spatial | Squidpy, Scanpy, Moran's I, neighbourhood |
| 02-07 | Pooled CRISPR Screens | Single-cell & Spatial | sgRNA→cell map, glmGamPoi, batch correction |
| 02-08 | scRNA Disease Drug Discovery | Single-cell & Spatial | pseudobulk DE, decoupler, liana-py, Open Targets |
| 03-01 | Variant Annotation | Population Genetics & Genomics | Ensembl VEP, SnpEff, ClinVar |
| 03-02 | GWAS to Function (TWAS) | Population Genetics & Genomics | TWAS, colocalization, MR, FUSION |
| 03-03 | Mendelian Randomization | Population Genetics & Genomics | IVW, MR-Egger, weighted median, OpenGWAS |
| 03-04 | Polygenic Risk Score | Population Genetics & Genomics | PGS Catalog, 1000 Genomes, multi-trait |
| 04-01 | MS Differential Proteins | Proteomics & Multi-omics | limma, DEqMS, MinProb / kNN |
| 04-02 | Serum Proteomics, Longitudinal | Proteomics & Multi-omics | MNAR test, Wilcoxon, mixed-effects, DTW |
| 04-03 | Multi-omics Integration | Proteomics & Multi-omics | MOFA2, mixOmics |
| 04-04 | Protein Structure Collector | Proteomics & Multi-omics | UniProt, RCSB PDB API, AlphaFold EBI |
| 05-01 | Peak Enrichment (genes → TF) | Epigenomics & Gene Regulation | ChIP-Atlas API, Fisher, BH |
| 05-02 | Target Genes (TF → genes) | Epigenomics & Gene Regulation | MACS2 score, cell-type filter, STRING |
| 05-03 | Differential Peaks / DMR | Epigenomics & Gene Regulation | edgeR (DPR), metilene (DMR), BED |
| 05-04 | Upstream Regulator Analysis | Epigenomics & Gene Regulation | Fisher overlap, directionality, combined score |
| 06-01 | Clinical Survival Analysis | Clinical & Biostatistics | Kaplan-Meier, Cox PH, Schoenfeld |
| 06-02 | Disease Progression | Clinical & Biostatistics | TimeAx, disease pseudotime |
| 06-03 | LASSO Biomarker Panel | Clinical & Biostatistics | elastic net, nested CV, stability selection |
| 06-04 | Experimental Design & Stats | Clinical & Biostatistics | power analysis, IHW, batch balancing |
| 06-05 | Microplate Layout | Clinical & Biostatistics | randomization, edge-effect, covariate balance |
| 07-01 | PCR Primer Design | Experimental Design & Molecular Biology | Primer3, Primer-BLAST, Tm / GC checks |
| 07-02 | sgRNA Design | Experimental Design & Molecular Biology | Addgene, CRISPick, de-novo rules |
| 07-03 | C. elegans Feeding RNAi | Experimental Design & Molecular Biology | auto sequence, restriction adapters, 4-axis score |
| 08-01 | Omics Dataset Retrieval | Databases, Literature & Drug Discovery | GEO, TCGA, multi-repo search |
| 08-02 | Open Targets (GraphQL) | Databases, Literature & Drug Discovery | GraphQL API, FAERS, evidence integration |
| 08-03 | Clinical Trials Landscape | Databases, Literature & Drug Discovery | ClinicalTrials API v2, MoA classification |
| 08-04 | Preclinical Literature Mining | Databases, Literature & Drug Discovery | Consensus, in vitro / in vivo, synthesis |
| 08-05 | Phylogenetics Toolkit | Databases, Literature & Drug Discovery | MSA, IQ-TREE, ancestral recon, Newick |
| 08-06 | Meta: Create a Skill | Databases, Literature & Drug Discovery | create, test, package, present |