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By FreedomIntelligence
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 193 | Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 194 | Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 195 | Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 196 | 196.Deep Research Execute autonomous multi-step deep research on any topic. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 197 | Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology frameworks. | FreedomIntelligence/ | 3.1k | 1 repo | ~8.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 198 | 198.Chemist Analyst Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). | FreedomIntelligence/ | 3.1k | 1 repo | ~13k | Automated safety check: Pass | No licence | 2 mo ago |
| 199 | Analyzes disease patterns and health events through epidemiological lens using surveillance systems, outbreak investigation methods, and disease modeling frameworks. | FreedomIntelligence/ | 3.1k | 1 repo | ~18k | Automated safety check: Pass | No licence | 2 mo ago |
| 200 | Analyzes events through psychological lens using cognitive psychology, social psychology, developmental psychology, clinical psychology, and neuroscience. | FreedomIntelligence/ | 3.1k | 1 repo | ~15k | Automated safety check: Pass | No licence | 2 mo ago |
| 201 | Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports. | FreedomIntelligence/ | 3.1k | 2 repos | ~2.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 202 | 202.Labstep Interact with the Labstep electronic lab notebook API using labstepPy. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 203 | Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages. | FreedomIntelligence/ | 3.1k | 1 repo | ~969 | Automated safety check: Pass | MIT | 2 mo ago |
| 204 | 204.Patiently AI Patiently AI simplifies medical documents for patients. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~986 | Automated safety check: Pass | No licence | 2 mo ago |
| 205 | Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files. | FreedomIntelligence/ | 3.1k | 1 repo | ~850 | Automated safety check: Pass | No licence | 2 mo ago |
| 206 | 206.Usmle Prepare for US medical licensing exams with progress tracking, weak area analysis, question bank management, and residency match planning. | FreedomIntelligence/ | 3.1k | 1 repo | ~670 | Automated safety check: Pass | No licence | 2 mo ago |
| 207 | Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations. | FreedomIntelligence/ | 3.1k | 1 repo | ~936 | Automated safety check: Pass | No licence | 2 mo ago |
| 208 | Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against… | FreedomIntelligence/ | 3.1k | 1 repo | ~1.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 209 | Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation. | FreedomIntelligence/ | 3.1k | 1 repo | ~921 | Automated safety check: Pass | No licence | 2 mo ago |
| 210 | Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes. | FreedomIntelligence/ | 3.1k | 1 repo | ~971 | Automated safety check: Pass | No licence | 2 mo ago |
| 211 | Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 212 | Gene set enrichment analysis with correct geneset format handling. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 213 | Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities. | FreedomIntelligence/ | 3.1k | 1 repo | ~3.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 214 | Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 215 | Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in… | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 216 | Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 217 | Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq… | FreedomIntelligence/ | 3.1k | 1 repo | ~3.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 218 | Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists. | FreedomIntelligence/ | 3.1k | 1 repo | ~749 | Automated safety check: Pass | No licence | 2 mo ago |
| 219 | Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser. | FreedomIntelligence/ | 3.1k | 1 repo | ~353 | Automated safety check: Pass | MIT | 2 mo ago |
| 220 | An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literature reasoning. | FreedomIntelligence/ | 3.1k | 1 repo | ~416 | Automated safety check: Pass | MIT | 2 mo ago |
| 221 | Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. | FreedomIntelligence/ | 3.1k | — | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 222 | Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. | FreedomIntelligence/ | 3.1k | — | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 223 | Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. | FreedomIntelligence/ | 3.1k | — | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 224 | Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. | FreedomIntelligence/ | 3.1k | — | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 225 | Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. | FreedomIntelligence/ | 3.1k | — | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 226 | Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. | FreedomIntelligence/ | 3.1k | — | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 227 | Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. | FreedomIntelligence/ | 3.1k | — | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 228 | 228.Bio Chipseq Qc ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate… | FreedomIntelligence/ | 3.1k | — | ~2.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 229 | Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. | FreedomIntelligence/ | 3.1k | — | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 230 | Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. | FreedomIntelligence/ | 3.1k | — | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 231 | Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. | FreedomIntelligence/ | 3.1k | — | ~1.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 232 | Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. | FreedomIntelligence/ | 3.1k | — | ~1.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 233 | Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. | FreedomIntelligence/ | 3.1k | — | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 234 | Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. | FreedomIntelligence/ | 3.1k | — | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 235 | Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. | FreedomIntelligence/ | 3.1k | — | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 236 | Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. | FreedomIntelligence/ | 3.1k | — | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 237 | Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. | FreedomIntelligence/ | 3.1k | — | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 238 | Annotate CNVs with genes, pathways, and clinical significance. | FreedomIntelligence/ | 3.1k | — | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 239 | Detect copy number variants from targeted/exome sequencing using CNVkit. | FreedomIntelligence/ | 3.1k | — | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 240 | Statistical methods for calling hits in CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | — | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
