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Research & Science · By FreedomIntelligence
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 97 | Quality control and assessment for proteomics data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 98 | RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 99 | Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 100 | Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 101 | Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 102 | Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 103 | Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). | FreedomIntelligence/ | 3.1k | 1 repo | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 104 | Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.4k | Automated safety check: Pass | No licence | 2 mo ago |
| 105 | Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 106 | Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 107 | Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 108 | Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 109 | Compute spatial statistics for spatial transcriptomics data using Squidpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 110 | Visualize spatial transcriptomics data using Squidpy and Scanpy. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 111 | Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 112 | 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 |
| 113 | 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 |
| 114 | 114.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 |
| 115 | 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 |
| 116 | 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 |
| 117 | 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 |
| 118 | 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 |
| 119 | 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 |
| 120 | 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 |
| 121 | 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 |
| 122 | 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 |
| 123 | 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 |
| 124 | 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 |
| 125 | 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 |
| 126 | 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 |
| 127 | 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 |
| 128 | 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 |
| 129 | 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 |
| 130 | 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 |
| 131 | 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 |
| 132 | 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 |
| 133 | 133.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 |
| 134 | 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 |
| 135 | Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. | FreedomIntelligence/ | 3.1k | — | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 136 | 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 |
| 137 | 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 |
| 138 | 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 |
| 139 | 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 |
| 140 | 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 |
| 141 | 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 |
| 142 | MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. | FreedomIntelligence/ | 3.1k | — | ~1.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 143 | Quality control for pooled CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | — | ~2.1k | Automated safety check: Pass | No licence | 2 mo ago |
| 144 | Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. | FreedomIntelligence/ | 3.1k | — | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
