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Claude Skills by FridrichMethod
github.com/FridrichMethod743 skills4 installs957 views
- Bio Workflows Chipseq PipelineEnd-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.Votes: 0GitHub stars: 13
- Bio Workflows Clip PipelineEnd-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods.Votes: 0GitHub stars: 13
- Bio Workflows Cnv PipelineEnd-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.Votes: 0GitHub stars: 13
- Bio Workflows Crispr Editing PipelineEnd-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.Votes: 0GitHub stars: 13
- Bio Workflows Crispr Screen PipelineEnd-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods. Use when analyzing pooled CRISPR screens from count data to hit calling.Votes: 0GitHub stars: 13
- Bio Workflows Cytometry PipelineEnd-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.Votes: 0GitHub stars: 13
- Bio Workflows Expression To PathwaysWorkflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.Votes: 0GitHub stars: 13
- Bio Workflows Fastq To VariantsEnd-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.Votes: 0GitHub stars: 13
- Bio Workflows Genome Assembly PipelineEnd-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.Votes: 0GitHub stars: 13
- Bio Workflows Gwas PipelineEnd-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.Votes: 0GitHub stars: 13
- Bio Workflows Hic PipelineEnd-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization. Use when processing Hi-C data to compartments and TADs.Votes: 0GitHub stars: 13
- Bio Workflows Imc PipelineEnd-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.Votes: 0GitHub stars: 13
- Bio Workflows Longread Sv PipelineEnd-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.Votes: 0GitHub stars: 13
- Bio Workflows Merip PipelineEnd-to-end MeRIP-seq analysis from FASTQ to m6A peaks and differential methylation. Use when analyzing epitranscriptomic m6A modifications from immunoprecipitation data.Votes: 0GitHub stars: 13
- Bio Workflows Metabolic Modeling PipelineEnd-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.Votes: 0GitHub stars: 13
- Bio Workflows Metabolomics PipelineEnd-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping. Use when processing LC-MS metabolomics data.Votes: 0GitHub stars: 13
- Bio Workflows Metagenomics PipelineEnd-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.Votes: 0GitHub stars: 13
- Bio Workflows Methylation PipelineEnd-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.Votes: 0GitHub stars: 13
- Bio Workflows Microbiome PipelineEnd-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.Votes: 0GitHub stars: 13
- Bio Workflows Multi Omics PipelineEnd-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics datasets.Votes: 0GitHub stars: 13
- Bio Workflows Multiome PipelineEnd-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.Votes: 0GitHub stars: 13
- Bio Workflows Neoantigen PipelineEnd-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immunogenicity scoring. Use when identifying tumor neoantigens for personalized vaccine design or checkpoint biomarkers.Votes: 0GitHub stars: 13
- Bio Workflows Outbreak PipelineEnd-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.Votes: 0GitHub stars: 13
- Bio Workflows Proteomics PipelineEnd-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma. Use when processing mass spectrometry proteomics.Votes: 0GitHub stars: 13
- Bio Workflows Riboseq PipelineEnd-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.Votes: 0GitHub stars: 13
- Bio Workflows Rnaseq To DeEnd-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.Votes: 0GitHub stars: 13
- Bio Workflows Scrnaseq PipelineEnd-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.Votes: 0GitHub stars: 13
- Bio Workflows Smrna PipelineEnd-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.Votes: 0GitHub stars: 13
- Bio Workflows Somatic Variant PipelineEnd-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics. Use when calling somatic mutations from tumor-normal pairs.Votes: 0GitHub stars: 13
- Bio Workflows Spatial PipelineEnd-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy. Use when analyzing spatial transcriptomics data.Votes: 0GitHub stars: 13
- Bio Workflows Tcr PipelineEnd-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.Votes: 0GitHub stars: 13
- Bioinformatics SinglecellAdvanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq. Use when analyzing single-cell data, cell type identification, trajectory analysis, differential expression, UMAP/clustering, integrating protein and RNA modalities (TotalVI), or working with Scanpy, Seurat, scvi-tools. Includes workflows for MPN, hematologic malignancies, megakaryocyte biology.Votes: 0GitHub stars: 13
- BiokernelBiomedical OS Core & MCP ServerVotes: 0GitHub stars: 13
- Biologist Analyst"Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology,Votes: 0GitHub stars: 13
- Biomaster WorkflowsPipeline maestroVotes: 0GitHub stars: 13
- Biomcp ServerMCP bio bridgeVotes: 0GitHub stars: 13
- Biomedical Data AnalysisOmics data forgeVotes: 0GitHub stars: 13
- Biomni General AgentUse the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.Votes: 0GitHub stars: 13
- Biomni Research AgentBio-Research GeneralistVotes: 0GitHub stars: 13
- Bioservices Multi DatabaseUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.Votes: 0GitHub stars: 13
- BlueprintTurn a one-line objective into a step-by-step construction plan for multi-session, multi-agent engineering projects. Each step has a self-contained context brief so a fresh agent can execute it cold. Includes adversarial review gate, dependency graph, parallel step detection, anti-pattern catalog, and plan mutation protocol. TRIGGER when: user requests a plan, blueprint, or roadmap for a complex multi-PR task, or describes work that needs multiple sessions. DO NOT TRIGGER when: task is comple...Votes: 0GitHub stars: 13
- Boltz"Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources.Votes: 0GitHub stars: 13
- Boltzgen"All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration.Votes: 0GitHub stars: 13
- Bone Marrow Ai AgentAI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images.Votes: 0GitHub stars: 13
- Brand LandingpageBrand-first landing page designer — runs a brand-identity interview (colors, typography, shape language), then generates and iterates on a polished landing page via Stitch with deployment-ready HTML. Use when the user asks to create, design, or build a landing page, homepage, or marketing page and has no established visual direction. Skip when they have a design mockup, need a dashboard or app UI, are working at component level, building a multi-page app, or restyling with known design tokens...Votes: 0GitHub stars: 13
- Campaign Manager"Goal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target.Votes: 0GitHub stars: 13
- Cancer Metabolism AgentAI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilities for therapeutic targeting.Votes: 0GitHub stars: 13
- Care CoordinationCare Coordination agent for healthcare workflows.Votes: 0GitHub stars: 13
- Carrier Relationship ManagementCodified expertise for managing carrier portfolios, negotiating freight rates, tracking carrier performance, allocating freight, and maintaining strategic carrier relationships. Informed by transportation managers with 15+ years experience. Includes scorecarding frameworks, RFP processes, market intelligence, and compliance vetting. Use when managing carriers, negotiating rates, evaluating carrier performance, or building freight strategies.Votes: 0GitHub stars: 13
- Cart Design Optimizer AgentAI-guided CAR-T cell design for solid tumors using antigen prioritization, safety-by-design architectures, and exhaustion-resistant engineering.Votes: 0GitHub stars: 13