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All 15 Skills
Each skill encodes domain-expert decisions — correct tool versions, QC thresholds, and normalization methods. The AI never guesses at bioinformatics parameters.
| # | Skill | Data Type | Key Tools | Status |
|---|---|---|---|---|
| 1 | Genomics | WGS / WES / SNP | GATK 4.4, bcftools, plink 2.0, VEP 110 | Stable |
| 2 | Transcriptomics | Bulk RNA-seq | DESeq2 1.40, salmon 1.10, edgeR | Stable |
| 3 | scRNA-seq | Single-cell RNA | Scanpy 1.9, Seurat 5, leidenalg | Stable |
| 4 | Proteomics | LC-MS/MS DDA+DIA | MaxQuant 2.4, DIA-NN 1.8, limma | Stable |
| 5 | Metabolomics | LC-MS / GC-MS | XCMS 3.22, MZmine 3.4, MetaboAnalyst | Stable |
| 6 | Bulk Epigenomics | Bulk ATAC + ChIP-seq | MACS3 3.0, deepTools 3.5, DiffBind | Stable |
| 7 | Spatial v1 | Visium | Squidpy 1.4, SpatialDE | Stable |
| 8 | Metagenomics | Shotgun / 16S | MetaPhlAn 4.0, Kraken2, DADA2 | Stable |
| 9 | sc-Proteomics | CITE-seq ADT | Seurat 5 WNN, CITE-seq-Count | Stable |
| 10 | Integration | Multi-omics | MOFA+ 1.6, mixOmics (DIABLO) | Stable |
| 11 | scATAC-seq | Single-cell ATAC | ArchR 1.0, ChromVAR 1.22, Signac | New v0.2 |
| 12 | Bulk Epigenomics Full | 6 histone marks + ATAC | deepTools 3.5, DiffBind, HOMER | New v0.2 |
| 13 | Spatial Full | Visium/MERFISH/CosMx/Stereo-seq | Squidpy, cell2location, CellChat | New v0.2 |
| 14 | scTCR/BCR-seq | Immune repertoire | Scirpy 0.16, IgBlast, Immcantation | New v0.2 |
| 15 | sc-Proteomics Full | CITE-seq ADT + SCoPE-MS | Seurat 5, limma, MaxQuant 2.4 | New v0.2 |