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Claude Skills by David-Li0406
github.com/David-Li04065,064 skills17 installs250 views
- Bio Tcr Bcr Analysis Mixcr AnalysisPerform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.Votes: 0GitHub stars: 2
- Bio Tcr Bcr Analysis Repertoire VisualizationCreate publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Use when generating figures for repertoire comparisons, clonal dynamics, or V(D)J gene usage.Votes: 0GitHub stars: 2
- Bio Tcr Bcr Analysis Scirpy AnalysisAnalyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating immune receptor information with cell state analysis.Votes: 0GitHub stars: 2
- Bio Tcr Bcr Analysis Vdjtools AnalysisCalculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.Votes: 0GitHub stars: 2
- Bio Transcription TranslationTranscribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.Votes: 0GitHub stars: 2
- Bio Uniprot AccessAccess UniProt protein database for sequences, annotations, and functional information. Use when you need protein data, GO terms, domain annotations, or protein-protein interactions.Votes: 0GitHub stars: 2
- Bio Variant Calling Clinical InterpretationClinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.Votes: 0GitHub stars: 2
- Bio Variant Calling Structural Variant CallingCall structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data.Votes: 0GitHub stars: 2
- Bio Variant CallingCall SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.Votes: 0GitHub stars: 2
- Bio Variant NormalizationNormalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.Votes: 0GitHub stars: 2
- Bio Vcf BasicsView, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.Votes: 0GitHub stars: 2
- Bio Vcf ManipulationMerge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.Votes: 0GitHub stars: 2
- Bio Vcf StatisticsGenerate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.Votes: 0GitHub stars: 2
- Bio Workflow Management Snakemake WorkflowsBuild reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-based workflows, automating multi-step analyses with make-like dependency tracking, or running pipelines on HPC clusters with SLURM.Votes: 0GitHub stars: 2
- Bio Workflows Atacseq PipelineEnd-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.Votes: 0GitHub stars: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- 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: 2
- Bio Write SequencesWrite biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.Votes: 0GitHub stars: 2
- Bioinformatics FundamentalsCore bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.Votes: 0GitHub stars: 2
- Bioinformatics PrimitivesUse biometal streaming primitives for ALL bioinformatics tasks. Trigger when parsing BAM/SAM/CRAM, FASTQ/FASTA, VCF/BCF, BED, GFF3/GTF, GFA, PAF files, calculating GC content, quality filtering, k-mer operations, or any genomics analysis. NEVER use subprocess calls to samtools, bcftools, bedtools, or other CLI tools. Always use typed biometal functions instead.Votes: 0GitHub stars: 2
- Biome To OxcMigrate JavaScript/TypeScript projects from Biome to oxlint + oxfmt with Prettier fallback. Use when user asks to "migrate to oxlint", "switch from biome to oxc", "use oxfmt", or wants to adopt the oxc toolchain for linting and formatting.Votes: 0GitHub stars: 2
- Biorxiv Database 3Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.Votes: 0GitHub stars: 2
- Bioservices 3Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.Votes: 0GitHub stars: 2
- BitsTrack and manage work items, tasks, issues, and todos with dependencies using bits. Use when user needs to create tasks, track progress, manage blockers, find ready work, claim/release tasks, close completed work, or organize multi-step projects. Triggers on "bits", "task", "issue", "backlog", "blockers", "dependencies", "what's ready", "track this", "add to my list", "what should I work on".Votes: 0GitHub stars: 2
- Bitwarden SecretsRetrieve and manage secrets using Bitwarden Secrets Manager CLI (bws). Trigger terms: bitwarden, secrets, bws, secret, api key, credentials, password.Votes: 0GitHub stars: 2
- Biz GrowthHigh-performance business writing, content creation, and strategic growth constraints.Votes: 0GitHub stars: 2
- Biz Opportunity ScoutIdentify and validate profitable business opportunities by analyzing market size (TAM/SAM/SOM), unit economics, competitive landscape, and PMF indicators. Generates comprehensive HTML reports with opportunity scorecards.Votes: 0GitHub stars: 2