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Claude Skills by anubhavg-icpl
github.com/anubhavg-icpl5,037 skills134 installs9,251 views
- Sci Clinical Decision SupportGenerate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug dev...Votes: 0GitHub stars: 8
- Sci Clinical ReportsWrite comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. Use when you need help with clinical reports.Votes: 0GitHub stars: 8
- Sci CobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. Use when you need help with cobrapy.Votes: 0GitHub stars: 8
- Sci Database LookupSearch 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/cli...Votes: 0GitHub stars: 8
- Sci DatamolPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly. Use when you need help with datamol.Votes: 0GitHub stars: 8
- Sci DeeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization. Use when you need help with deeptools.Votes: 0GitHub stars: 8
- Sci DiffdockDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction. Use when you need help with diffdock.Votes: 0GitHub stars: 8
- Sci Dnanexus IntegrationDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution. Use when you need help with dnanexus integration.Votes: 0GitHub stars: 8
- Sci EtetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics. Use when you need help with etetoolkit.Votes: 0GitHub stars: 8
- Sci Exploratory Data AnalysisPerform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scien...Votes: 0GitHub stars: 8
- Sci FlowioParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing. Use when you need help with flowio.Votes: 0GitHub stars: 8
- Sci Get Available ResourcesThis skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before runni...Votes: 0GitHub stars: 8
- Sci Ginkgo Cloud LabSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.Votes: 0GitHub stars: 8
- Sci GlycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design. Use when you need help with glycoengineering.Votes: 0GitHub stars: 8
- Sci Hugging ScienceUse when the user is doing AI/ML work in a scientific domain — biology, chemistry, physics, astronomy, climate, genomics, materials science, medicine, ecology, energy, conservation, engineering, mathematics, scientific reasoning, drug discovery, protein design, weather modeling, theorem proving, single-cell, PDE solving, or anything similar. Hugging Science (huggingscience.co) is a curated catalog of scientific datasets, models, blog posts, and interactive Spaces; the `hugging-science` org on...Votes: 0GitHub stars: 8
- Sci InfographicsCreate professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes. Use when you need help with infographics.Votes: 0GitHub stars: 8
- Sci Labarchive IntegrationElectronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows. Use when you need help with labarchive integration.Votes: 0GitHub stars: 8
- Sci Latchbio IntegrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration. Use when you need help with latchbio integration.Votes: 0GitHub stars: 8
- Sci Latex PostersCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication. Use when you need help with latex posters.Votes: 0GitHub stars: 8
- Sci Literature ReviewConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.). Use when you nee...Votes: 0GitHub stars: 8
- Sci Market Research ReportsGenerate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix. Use when you need help with market research reports.Votes: 0GitHub stars: 8
- Sci MarkitdownConvert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more. Use when you need help with markitdown.Votes: 0GitHub stars: 8
- Sci MedchemMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering. Use when you need help with medchem.Votes: 0GitHub stars: 8
- Sci Molecular DynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics. Use when you need help with molecular dynamics.Votes: 0GitHub stars: 8
- Sci MolfeatMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML. Use when you need help with molfeat.Votes: 0GitHub stars: 8
- Sci Omero IntegrationMicroscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows. Use when you need help with omero integration.Votes: 0GitHub stars: 8
- Sci Optimize For GpuGPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, KvikIO, cuCIM, cuxfilter, cuVS, cuSpatial, and RAFT. Use whenever the user mentions GPU/CUDA/NVIDIA acceleration, or wants to speed up NumPy, pandas, scikit-learn, scikit-image, NetworkX, GeoPandas, or Faiss workloads. Covers physics simulation, differentiable rendering, mesh ray casting, particle systems (DEM/SPH/fluids), vector/similarity search, GPUDirect Storage file IO, interactive dashboards, geospatial analys...Votes: 0GitHub stars: 8
- Sci Paper LookupSearch 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID lookups, abstracts, full text, open access, preprints, citation graphs, author search, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X" or "look up this DOI".Votes: 0GitHub stars: 8
- Sci Parallel WebAll-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources. Use this skill whenever the user needs to search the web, fetch/extract URL content, enrich data with web-sourced fields, or run deep research reports. Covers: web search (fast lookups, research, current info — prioritizing peer-reviewed papers, preprints, and scholarly databases), URL extraction (fetching pages, articles, academic PDFs), bulk data enrichment (adding fields to CSV/lists ...Votes: 0GitHub stars: 8
- Sci PhylogeneticsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies. Use when you need help with phylogenetics.Votes: 0GitHub stars: 8
- Sci Polars BioHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative. Use when you need help with polars bio.Votes: 0GitHub stars: 8
- Sci Pptx PostersCreate research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration. Use when you need help with pptx posters.Votes: 0GitHub stars: 8
- Sci PrimekgQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more. Use when you need help with primekg.Votes: 0GitHub stars: 8
- Sci Protocolsio IntegrationIntegration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation. Use...Votes: 0GitHub stars: 8
- Sci Pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis. Use when you need help with pydeseq2.Votes: 0GitHub stars: 8
- Sci PyhealthBuild clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNor...Votes: 0GitHub stars: 8
- Sci PymatgenMaterials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science. Use when you need help with pymatgen.Votes: 0GitHub stars: 8
- Sci PymcBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference. Use when you need help with pymc.Votes: 0GitHub stars: 8
- Sci PymooMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems. Use when you need help with pymoo.Votes: 0GitHub stars: 8
- Sci PysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines. Use when you need help with pysam.Votes: 0GitHub stars: 8
- Sci PytdcTherapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction. Use when you need help with pytdc.Votes: 0GitHub stars: 8
- Sci Pytorch LightningDeep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training. Use when you need help with pytorch lightning.Votes: 0GitHub stars: 8
- Sci RdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms. Use when you need help with rdkit.Votes: 0GitHub stars: 8
- Sci Research GrantsWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements. Use when you need help with research grants.Votes: 0GitHub stars: 8
- Sci Research LookupLook up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (deep research), or Perplexity sonar-pro-search (academic paper searches). Automatically routes queries to the best backend. Use for finding papers, gathering research data, and verifying scientific information. Note: query text is transmitted to api.parallel.ai (PARALLEL_API_KEY) and, for academic searches, to openrouter.ai (OPENROUTER_API_KEY).Votes: 0GitHub stars: 8
- Sci Scholar EvaluationSystematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback. Use when you need help with scholar evaluation.Votes: 0GitHub stars: 8
- Sci 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. Use when you need help with scientific schematics.Votes: 0GitHub stars: 8
- Sci Scientific SlidesBuild slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer. Use when you need help with scientific slides.Votes: 0GitHub stars: 8
- Sci Scientific WritingCore skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions. Use when you need help with scientific writing.Votes: 0GitHub stars: 8
- Sci Scikit BioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis. Use when you need help with scikit bio.Votes: 0GitHub stars: 8