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Claude Skills by mdbabumiamssm

github.com/mdbabumiamssm

1,581 skillsA× 1,569B× 10D× 1F× 13 installs3,534 views

Crispr Screen PipelineA--> --- name: bio-workflows-crispr-screen-pipeline description: End-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. tool_type: mixed primary_tool: MAGeCK workflow: true depends_on: - crispr-screens/screen-qc - crispr-screens/mageck-analysis - crispr-screens/hit-calling - crispr-screens/library-design - crispr-...datapythongoVotes: 0GitHub stars: 6
Cytometry PipelineA--> --- name: bio-workflows-cytometry-pipeline description: End-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. tool_type: r primary_tool: CATALYST workflow: true depends_on: - flow-cytometry/fcs-handling - flow-cytometry/compensation-transformation - flow-cytometry/gating-analysis - flow-cytometry/clus...datapythonshellVotes: 0GitHub stars: 6
Expression To PathwaysA--> --- name: bio-workflows-expression-to-pathways description: Workflow 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. tool_type: r primary_tool: clusterProfiler workflow: true depends_on: - pathway-analysis/go-enrichment - pathway-analysis/kegg-pathways - pathway-analysis/reactome-pathways - pathway-analysis/gsea - pathway-analysis/enrichmen...toolsgoshellVotes: 0GitHub stars: 6
Fastq To VariantsA--> --- name: bio-workflows-fastq-to-variants description: End-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. tool_type: cli primary_tool: bcftools workflow: true depends_on: - read-qc/fastp-workflow - read-alignment/bwa-alignment - alignment-files/alignment-sorting - alignment-files/duplicate-handling - variant-calli...toolsshellbashVotes: 0GitHub stars: 6
Genome Assembly PipelineA--> --- name: bio-workflows-genome-assembly-pipeline description: End-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. tool_type: cli primary_tool: Flye workflow: true depends_on: - read-qc/fastp-workflow - genome-assembly/short-read-assembly - genome-assembly/long-read-assembly - genome-assembly/assembly-polishing - genome-assembly/assembly-qc qc_checkp...toolsgoshellVotes: 0GitHub stars: 6
Gwas PipelineA--> --- name: bio-workflows-gwas-pipeline description: End-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. tool_type: mixed primary_tool: PLINK2 workflow: true depends_on: - population-genetics/plink-basics - population-genetics/population-structure - population-genetics/association-testing - population-genetics/linkage-dise...datashellbashVotes: 0GitHub stars: 6
Hic PipelineA--> --- name: bio-workflows-hic-pipeline description: End-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. tool_type: mixed primary_tool: cooler workflow: true depends_on: - hi-c-analysis/hic-data-io - hi-c-analysis/contact-pairs - hi-c-analysis/matrix-operations - hi-c-analysis/compartment-analysis - hi-c-analysis/tad-detection - hi-c-analys...datapythongoVotes: 0GitHub stars: 6
Imc PipelineA--> --- name: bio-workflows-imc-pipeline description: End-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. tool_type: python primary_tool: steinbock workflow: true depends_on: - imaging-mass-cytometry/data-preprocessing - imaging-mass-cytometry/cell-segmentation - imaging-mass-cytometry/phenotyping - imaging-mass-...datapythonshellVotes: 0GitHub stars: 6
Liquid Biopsy PipelineA--> --- name: bio-liquid-biopsy-pipeline description: Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring. tool_type: mixed primary_tool: ichorCNA measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tool...toolspythongoVotes: 0GitHub stars: 6
Longread Sv PipelineA--> --- name: bio-workflows-longread-sv-pipeline description: End-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. tool_type: cli primary_tool: Sniffles workflow: true depends_on: - long-read-sequencing/long-read-alignment - long-read-sequencing/long-read-qc - long-read-sequencing/structural-variants qc_checkpoints: - after_...toolsgoshellVotes: 0GitHub stars: 6
Merip PipelineA--> --- name: bio-workflows-merip-pipeline description: End-to-end MeRIP-seq analysis from FASTQ to m6A peaks and differential methylation. Use when analyzing epitranscriptomic m6A modifications from immunoprecipitation data. tool_type: mixed primary_tool: exomePeak2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---toolsshellbashVotes: 0GitHub stars: 6
Metabolic Modeling PipelineA--> --- name: bio-workflows-metabolic-modeling-pipeline description: End-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. tool_type: mixed primary_tool: cobrapy workflow: true depends_on: - systems-biology/metabolic-reconstruction - systems-biology...testingpythonshellVotes: 0GitHub stars: 6
Metabolomics PipelineA--> --- name: bio-workflows-metabolomics-pipeline description: End-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. tool_type: r primary_tool: XCMS workflow: true depends_on: - metabolomics/xcms-preprocessing - metabolomics/metabolite-annotation - metabolomics/normalization-qc - metabolomics/statistical-analysis - metabolomics/pa...datashelltestingVotes: 0GitHub stars: 6
Metagenomics PipelineA--> --- name: bio-workflows-metagenomics-pipeline description: End-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. tool_type: cli primary_tool: Kraken2 workflow: true depends_on: - read-qc/fastp-workflow - metagenomics/kraken-classification - metagenomics/metaphlan-profiling - metagenomics/abundance-estimation - metagenomics/functi...toolspythonshellVotes: 0GitHub stars: 6
Methylation PipelineA--> --- name: bio-workflows-methylation-pipeline description: End-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. tool_type: mixed primary_tool: Bismark workflow: true depends_on: - read-qc/fastp-workflow - methylation-analysis/bismark-alignment - methylation-analysis/methylation-calling - methylation-analysis/methylkit-analysis -...toolsgoshellVotes: 0GitHub stars: 6
Microbiome PipelineA--> --- name: bio-workflows-microbiome-pipeline description: End-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. tool_type: r primary_tool: dada2 workflow: true depends_on: - microbiome/amplicon-processing - microbiome/taxonomy-assignment - microbiome/diversity-analysis - microbiome/differential-abundance measurab...datarustgoVotes: 0GitHub stars: 6
Multi Omics PipelineA--> --- name: bio-workflows-multi-omics-pipeline description: End-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. tool_type: r primary_tool: MOFA2 workflow: true depends_on: - multi-omics-integration/data-harmonization - multi-omics-integration/mofa-integration - multi-omics-int...datagoshellVotes: 0GitHub stars: 6
Multiome PipelineA--> --- name: bio-workflows-multiome-pipeline description: End-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. tool_type: r primary_tool: Seurat workflow: true depends_on: - single-cell/data-io - single-cell/preprocessing - single-cell/clustering - single-cell/multimodal-integration - single-cell/scatac-analysis qc_checkpoints: - after_load...toolsgoshellVotes: 0GitHub stars: 6
Neoantigen PipelineA--> --- name: bio-workflows-neoantigen-pipeline description: End-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. tool_type: mixed primary_tool: pVACtools workflow: true depends_on: - clinical-databases/hla-typing - immunoinformatics/mhc-binding-prediction - immun...toolspythongoVotes: 0GitHub stars: 6
Outbreak PipelineA--> --- name: bio-workflows-outbreak-pipeline description: End-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. tool_type: mixed primary_tool: mlst workflow: true depends_on: - epidemiological-genomics/pathogen-typing - epidemiological-genomics/amr-surveillance - epidemiolog...toolspythongoVotes: 0GitHub stars: 6
Proteomics PipelineA--> --- name: bio-workflows-proteomics-pipeline description: End-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. tool_type: mixed primary_tool: MSstats workflow: true depends_on: - proteomics/data-import - proteomics/proteomics-qc - proteomics/quantification - proteomics/protein-inference - proteomics/different...datashelltestingVotes: 0GitHub stars: 6
Riboseq PipelineA--> --- name: bio-workflows-riboseq-pipeline description: End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation. tool_type: mixed primary_tool: Plastid measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---toolspythonshellVotes: 0GitHub stars: 6
Rnaseq To DeA--> --- name: bio-workflows-rnaseq-to-de description: End-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. tool_type: mixed primary_tool: DESeq2 workflow: true depends_on: - read-qc/fastp-workflow - rna-quantification/alignment-free-quant - rna-quantification/tximport-workflow - differential-expression/deseq2-basics - ...datagoshellVotes: 0GitHub stars: 6
Scrnaseq PipelineA--> --- name: bio-workflows-scrnaseq-pipeline description: End-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. tool_type: mixed primary_tool: Seurat workflow: true depends_on: - single-cell/data-io - single-cell/preprocessing - single-cell/doublet-detection - single-cell/clustering - single-cell/markers-annotation qc_checkpoints: - ...toolspythonshellVotes: 0GitHub stars: 6
Smrna PipelineA--> --- name: bio-workflows-smrna-pipeline description: End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data. tool_type: mixed primary_tool: miRDeep2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---toolsshellbashVotes: 0GitHub stars: 6
Somatic Variant PipelineA--> --- name: bio-workflows-somatic-variant-pipeline description: End-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. tool_type: cli primary_tool: GATK Mutect2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Comp...toolsshellbashVotes: 0GitHub stars: 6
Spatial PipelineA--> --- name: bio-workflows-spatial-pipeline description: End-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. tool_type: python primary_tool: Squidpy workflow: true depends_on: - spatial-transcriptomics/spatial-data-io - spatial-transcriptomics/spatial-preprocessing - spatial-transcriptomics/spatial-neighbors - spatial-transcr...datapythonshellVotes: 0GitHub stars: 6
Splicing PipelineA--> --- name: bio-splicing-pipeline description: End-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differential analysis, and generates sashimi visualizations. Use when performing comprehensive splicing analysis from raw RNA-seq data. tool_type: mixed primary_tool: rMATS-turbo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...datapythonshellVotes: 0GitHub stars: 6
Tcr PipelineA--> --- name: bio-workflows-tcr-pipeline description: End-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. tool_type: cli primary_tool: MiXCR measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---toolsshellbashVotes: 0GitHub stars: 6
OfficecliAgentOfficeAutomation AgentA-->  --- name: 'officecli-agent-office-automation' description: 'Use OfficeCLI to read, edit, and automate Word, Excel, and PowerPoint files through a single agent-friendly CLI without requiring Microsoft Office.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---businessshellgitVotes: 0GitHub stars: 6
Technical WritingA--> --- name: technical-writing-expert description: Create comprehensive, clear, and structured technical documentation, reports, and whitepapers. keywords: - documentation - reporting - markdown - latex - clarity - structure measurable_outcome: Produce a 2000-word technical report with <1% grammatical errors and >90% clarity score (Flesch-Kincaid) within 1 hour. license: MIT metadata: author: AI Agentic Skills Team version: "2.0.0" compatibility: - system: any allowed-tools: - read_file - wr...documentationgobashVotes: 0GitHub stars: 6