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Claude Skills by FreedomIntelligence
github.com/FreedomIntelligence741 skills2 installs1,922 views
- Repro EnforcerExport any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.Votes: 0GitHub stars: 2,984
- Research Literature--> --- name: 'research-literature' description: 'Research Literature agent for healthcare workflows.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill implements the Research Literature workflow using Anthropic's Claude.Votes: 0GitHub stars: 2,984
- Rna Velocity Agent--> --- name: 'rna-velocity-agent' description: 'AI-powered RNA velocity analysis for predicting cellular state transitions, differentiation trajectories, and dynamic gene regulation from single-cell RNA sequencing data.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **RNA Velocity Agent** analyzes RNA velocity from single-cell RNA sequencing to predict cellular state transitions, differentia...Votes: 0GitHub stars: 2,984
- Scfoundation Model Agent--> --- name: 'scfoundation-model-agent' description: 'Unified agent for leveraging single-cell foundation models (scGPT, scBERT, Geneformer, scFoundation) for cross-species annotation, perturbation prediction, and gene network inference.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **scFoundation Model Agent** provides a unified interface to leverage state-of-the-art single-cell foundation...Votes: 0GitHub stars: 2,984
- Scientific Manuscript--> --- name: scientific-manuscript description: "High-impact scientific manuscript preparation for journals like Nature, Blood, Cell. Use when writing abstracts, introductions, methods, results, discussions, or figure legends. Includes citation management, statistical reporting standards, ICMJE guidelines, and journal-specific formatting for hematology/oncology publications." license: Proprietary ---Votes: 0GitHub stars: 2,984
- Scientific SchematicsCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.Votes: 0GitHub stars: 2,984
- Scrna OrchestratorLocal Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.Votes: 0GitHub stars: 2,984
- Scrna Qc--> --- name: scrna-qc description: Execute the MAD-based single-cell RNA-seq QC workflow (scripts + Python API) to filter low-quality cells and emit reports plus filtered AnnData files. measurable_outcome: Produce filtered .h5ad files, before/after plots, and qc_summary.json within 20 minutes per dataset. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- ScveloRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.Votes: 0GitHub stars: 2,984
- SeabornStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.Votes: 0GitHub stars: 2,984
- Search Strategy--> --- name: search-strategy description: Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific syntax, ranks results by relevance, and handles ambiguity and fallback strategies. keywords: - search - query-decomposition - ranking - multi-source - strategy measurable_outcome: Successfully decomposes 100% of complex queries into source-specific sub-queries targeting relevant databa...Votes: 0GitHub stars: 2,984
- Seq WranglerSequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.Votes: 0GitHub stars: 2,984
- Simo Multiomics Integration Agent--> --- name: 'simo-multiomics-integration-agent' description: 'AI-powered spatial integration of multi-omics datasets using probabilistic alignment for comprehensive tissue atlas construction and cellular state mapping.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **SIMO Multiomics Integration Agent** performs spatial integration of multi-omics datasets through probabilistic alignment. Unl...Votes: 0GitHub stars: 2,984
- Simulation OrchestratorOrchestrate multi-simulation campaigns including parameter sweeps, batch jobs, and result aggregation. Use for running parameter studies, managing simulation batches, tracking job status, combining results from multiple runs, or automating simulation workflows.Votes: 0GitHub stars: 2,984
- Simulation ValidatorValidate simulations before, during, and after execution. Use for pre-flight checks, runtime monitoring, post-run validation, diagnosing failed simulations, checking convergence, detecting NaN/Inf, or verifying mass/energy conservation.Votes: 0GitHub stars: 2,984
- Single AnnotationGuide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.Votes: 0GitHub stars: 2,984
- Single Cellphone DbRun omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.Votes: 0GitHub stars: 2,984
- Single ClusteringGuide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.Votes: 0GitHub stars: 2,984
- Single Downstream AnalysisChecklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.Votes: 0GitHub stars: 2,984
- Single MultiomicsQuick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.Votes: 0GitHub stars: 2,984
- Single PreprocessingWalk 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.Votes: 0GitHub stars: 2,984
- Single To Spatial MappingMap scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.Votes: 0GitHub stars: 2,984
- Single TrajectoryGuide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.Votes: 0GitHub stars: 2,984
- Slurm Job Script GeneratorGenerate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when preparing submission scripts, deciding MPI vs MPI+OpenMP layouts, standardizing `#SBATCH` directives, or debugging job launch configuration (`sbatch`/`srun`).Votes: 0GitHub stars: 2,984
- Spatial Agent--> --- name: 'spatial-agent' description: 'An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- SpatialAgent focuses on the biological interpretation of spatial transcriptomics data, specifically aiming to propose mechanistic hypotheses about tissue organization and cellular interac...Votes: 0GitHub stars: 2,984
- Spatial Epigenomics Agent--> --- name: 'spatial-epigenomics-agent' description: 'AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Spatial Epigenomics Agent** analyzes spatial epigenomic data combining chromatin accessibility (ATAC-seq), histone...Votes: 0GitHub stars: 2,984
- Spatial Transcriptomics Agent--> --- name: spatial-transcriptomics-agent description: Spatial analyst keywords: - spatial - h5ad - H&E - clustering - SVG measurable_outcome: For each sample, deliver ≥1 spatial domain map + SVG list + narrative interpretation within 30 minutes. license: MIT metadata: author: LiuLab version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - read_file - web_fetch --- Run STAgent to align histology images with expression matrices, perform clustering/SVG detect...Votes: 0GitHub stars: 2,984
- Spatial Transcriptomics Analysis--> --- name: spatial-transcriptomics-analysis description: Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression. keywords: - spatial-transcriptomics - visium - xenium - scanpy - squidpy measurable_outcome: Process a Visium dataset, identify spatially variable genes, and generate spatial feature plots within 30 minutes. license: MIT metadata: author: MD BABU MIA, PhD version: "1.0.0" compatibility: - system: python 3.9+ allowed-too...Votes: 0GitHub stars: 2,984
- Image Analysis--> --- name: bio-spatial-transcriptomics-image-analysis description: Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_comma...Votes: 0GitHub stars: 2,984
- Spatial Communication--> --- name: bio-spatial-transcriptomics-spatial-communication description: Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling, identify communication pathways, and visualize interaction networks. Use when analyzing cell-cell communication in spatial context. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: ...Votes: 0GitHub stars: 2,984
- Spatial Data Io--> --- name: bio-spatial-transcriptomics-spatial-data-io description: Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other spatial data. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file...Votes: 0GitHub stars: 2,984
- Spatial Deconvolution--> --- name: bio-spatial-transcriptomics-spatial-deconvolution description: Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type proportions from scRNA-seq references. Use when estimating cell type composition in spatial spots. tool_type: python primary_tool: cell2location measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: ...Votes: 0GitHub stars: 2,984
- Spatial Domains--> --- name: bio-spatial-transcriptomics-spatial-domains description: Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering both expression and spatial context to define anatomical regions. Use when identifying tissue domains or spatial regions. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_comm...Votes: 0GitHub stars: 2,984
- Spatial Multiomics--> --- name: bio-spatial-transcriptomics-spatial-multiomics description: Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- Spatial Neighbors--> --- name: bio-spatial-transcriptomics-spatial-neighbors description: Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---...Votes: 0GitHub stars: 2,984
- Spatial Preprocessing--> --- name: bio-spatial-transcriptomics-spatial-preprocessing description: Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identify highly variable genes. Use when filtering and normalizing spatial transcriptomics data. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file ...Votes: 0GitHub stars: 2,984
- Spatial Proteomics--> --- name: bio-spatial-transcriptomics-spatial-proteomics description: Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics. tool_type: python primary_tool: scimap measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file...Votes: 0GitHub stars: 2,984
- Spatial Statistics--> --- name: bio-spatial-transcriptomics-spatial-statistics description: Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment. Use when computing spatial autocorrelation or co-occurrence statistics. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_...Votes: 0GitHub stars: 2,984
- Spatial Visualization--> --- name: bio-spatial-transcriptomics-spatial-visualization description: Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns. tool_type: python primary_tool: squidpy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Create visualizations f...Votes: 0GitHub stars: 2,984
- Spatial TutorialsGuide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.Votes: 0GitHub stars: 2,984
- Speech Pathology AiExpert speech-language pathologist specializing in AI-powered speech therapy, phoneme analysis, articulation visualization, voice disorders, fluency intervention, and assistive communicationVotes: 0GitHub stars: 2,984