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bio-tcr-bcr-analysis-vdjtools-analysis
Reference examples tested with: MiXCR 4.6+, VDJtools 1.2.1+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed v...
bio-variant-calling-filtering-best-practices
Reference examples tested with: GATK 4.5+, bcftools 1.19+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ...
bio-variant-calling
Reference examples tested with: bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: CLI: <tool> --version ...
bio-vcf-manipulation
Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: Python: pip...
bio-vcf-statistics
Reference examples tested with: bcftools 1.19+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: Python: p...
bio-workflows-atacseq-pipeline
Complete workflow from raw ATAC-seq FASTQ files to accessibility peaks, differential analysis, and TF footprinting. FASTQ files [1. QC & Trimming] ---...
bio-workflows-biomarker-pipeline
Complete pipeline from expression data to validated biomarker panels with classifier. Expression matrix + Metadata [1. Data Preparation] -----> Standa...
bio-workflows-crispr-editing-pipeline
Complete workflow for CRISPR experiment design: from target gene to delivery-ready constructs with branching paths for different editing strategies. T...
bio-workflows-crispr-screen-pipeline
FASTQ Files ──> Guide Counting ──> Count Matrix ┌─────────────────────────────────────────────┐ │ crispr-screen-pipeline │ ├─────...
bio-workflows-cytometry-pipeline
FCS Files ──> Compensation ──> Transformation ──> Gated/Clustered Data ┌─────────────────────────────────────────────────┐ │ cytometry-pipe...
bio-workflows-expression-to-pathways
Convert differential expression results into biological insights through functional enrichment analysis. DE Results (gene list or ranked list) [1. Gen...
bio-workflows-fastq-to-variants
Complete pipeline from raw DNA sequencing FASTQ files to filtered variant calls. FASTQ files [1. QC & Trimming] -----> fastp [2. Alignment] --------->...