| 01-01 | DESeq2 Differential Expression | 01-01__bulk-rnaseq-counts-to-de-deseq2 | 14 | .json:1, .md:5, .r:8 |
| 01-02 | DE — Auto Method Selection | 01-02__bulk-rnaseq-differential-expression-multi-method | 15 | .json:1, .md:4, .r:10 |
| 01-03 | Functional Enrichment | 01-03__functional-enrichment-from-degs | 18 | .json:1, .md:7, .r:8, .txt:2 |
| 01-04 | Omics Clustering | 01-04__bulk-omics-clustering | 27 | .json:1, .md:9, .py:14, .r:3 |
| 01-05 | Co-expression Network | 01-05__coexpression-network | 22 | .json:1, .md:5, .r:14, .txt:2 |
| 02-01 | Scanpy Core Analysis | 02-01__scrnaseq-scanpy-core-analysis | 29 | .json:1, .md:10, .py:18 |
| 02-02 | Seurat Core Analysis | 02-02__scrnaseq-seurat-core-analysis | 38 | .json:1, .md:12, .r:23, .txt:2 |
| 02-03 | Trajectory & Pseudotime | 02-03__scrna-trajectory-inference | 11 | .json:1, .md:5, .py:5 |
| 02-04 | Cell–Cell Communication | 02-04__cell-cell-communication | 9 | .json:1, .md:3, .r:5 |
| 02-05 | Regulatory Network (pySCENIC) | 02-05__grn-pyscenic | 11 | .json:1, .md:3, .py:7 |
| 02-06 | Spatial Transcriptomics | 02-06__spatial-transcriptomics | 7 | .json:1, .md:2, .py:4 |
| 02-07 | Pooled CRISPR Screens | 02-07__pooled-crispr-screens | 24 | .json:1, .md:6, .py:16, .r:1 |
| 02-08 | scRNA Disease Drug Discovery | 02-08__scrna-disease-drug-discovery | 19 | .json:1, .md:8, .py:10 |
| 03-01 | Variant Annotation | 03-01__genetic-variant-annotation | 30 | .json:1, .md:11, .py:16, .pyc:2 |
| 03-02 | GWAS to Function (TWAS) | 03-02__gwas-to-function-twas | 24 | .json:1, .md:9, .py:14 |
| 03-03 | Mendelian Randomization | 03-03__mendelian-randomization-twosamplemr | 9 | .json:1, .md:3, .r:5 |
| 03-04 | Polygenic Risk Score | 03-04__polygenic-risk-score-prs-catalog | 9 | .json:1, .md:3, .r:5 |
| 04-01 | MS Differential Proteins | 04-01__proteomics-diff-exp | 9 | .json:1, .md:3, .r:5 |
| 04-02 | Serum Proteomics, Longitudinal | 04-02__serum-proteomics-treatment-response | 9 | .json:1, .md:2, .r:6 |
| 04-03 | Multi-omics Integration | 04-03__multi-omics-integration | 7 | .json:1, .md:2, .r:4 |
| 04-04 | Protein Structure Collector | 04-04__protein-human-mouse-struct-collector | 3 | .html:1, .json:1, .md:1 |
| 05-01 | Peak Enrichment (genes → TF) | 05-01__chip-atlas-peak-enrichment | 15 | .json:1, .md:5, .py:9 |
| 05-02 | Target Genes (TF → genes) | 05-02__chip-atlas-target-genes | 13 | .json:2, .md:4, .py:7 |
| 05-03 | Differential Peaks / DMR | 05-03__chip-atlas-diff-analysis | 16 | .json:1, .md:4, .py:11 |
| 05-04 | Upstream Regulator Analysis | 05-04__upstream-regulator-analysis | 11 | .json:1, .md:2, .py:8 |
| 06-01 | Clinical Survival Analysis | 06-01__survival-analysis-clinical | 8 | .json:1, .md:3, .r:4 |
| 06-02 | Disease Progression | 06-02__disease-progression-longitudinal | 23 | .json:1, .md:8, .py:12, .r:2 |
| 06-03 | LASSO Biomarker Panel | 06-03__lasso-biomarker-panel | 14 | .json:1, .md:4, .py:1, .r:8 |
| 06-04 | Experimental Design & Stats | 06-04__experimental-design-statistics | 21 | .csv:1, .json:1, .md:8, .r:11 |
| 06-05 | Microplate Layout | 06-05__microplate-layout-design | 11 | .json:1, .md:5, .r:5 |
| 07-01 | PCR Primer Design | 07-01__pcr-primer-design | 18 | .json:1, .md:6, .py:11 |
| 07-02 | sgRNA Design | 07-02__sgrna-design | 13 | .csv:1, .json:1, .md:4, .py:6, .txt:1 |
| 07-03 | C. elegans Feeding RNAi | 07-03__celegans-rnai | 3 | .json:1, .md:2 |
| 08-01 | Omics Dataset Retrieval | 08-01__omics-dataset-retrieval | 2 | .json:1, .md:1 |
| 08-02 | Open Targets (GraphQL) | 08-02__Open Targets Platform (GraphQL API) | 2 | .json:1, .md:1 |
| 08-03 | Clinical Trials Landscape | 08-03__clinicaltrials-landscape | 14 | .json:1, .md:4, .py:9 |
| 08-04 | Preclinical Literature Mining | 08-04__literature-preclinical | 15 | .csv:2, .json:1, .md:2, .py:7, .r:1, .txt:2 |
| 08-05 | Phylogenetics Toolkit | 08-05__phylogenetics-toolkit | 2 | .json:1, .md:1 |
| 08-06 | Meta: Create a Skill | 08-06__phylo-create-skill | 2 | .json:1, .md:1 |