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Skills harvested from GitHub repositories
14810 skills availablebio-workflows-hic-pipeline
Complete workflow for Hi-C chromosome conformation capture analysis. Hi-C FASTQ files [1. Alignment & Pairs] --> bwa-mem...
bio-workflows-gwas-pipeline
Complete workflow for genome-wide association studies from genotype data to significant associations. VCF/PLINK files [1...
bio-workflows-genome-assembly-pipeline
Complete workflow from sequencing reads to polished, quality-assessed genome assembly. Reads (short and/or long) [1. QC ...
bio-workflows-fastq-to-variants
Complete pipeline from raw DNA sequencing FASTQ files to filtered variant calls. FASTQ files [1. QC & Trimming] -----> f...
bio-workflows-expression-to-pathways
Convert differential expression results into biological insights through functional enrichment analysis. DE Results (gen...
bio-workflows-cytometry-pipeline
FCS Files ──> Compensation ──> Transformation ──> Gated/Clustered Data ┌────────────────────────────────────────────────...
bio-workflows-crispr-screen-pipeline
FASTQ Files ──> Guide Counting ──> Count Matrix ┌─────────────────────────────────────────────┐ │ crispr-screen-...
bio-workflows-crispr-editing-pipeline
Complete workflow for CRISPR experiment design: from target gene to delivery-ready constructs with branching paths for d...
bio-workflows-biomarker-pipeline
Complete pipeline from expression data to validated biomarker panels with classifier. Expression matrix + Metadata [1. D...
bio-workflows-atacseq-pipeline
Complete workflow from raw ATAC-seq FASTQ files to accessibility peaks, differential analysis, and TF footprinting. FAST...
bio-vcf-statistics
Reference examples tested with: bcftools 1.19+, numpy 1.26+ Before using code patterns, verify installed versions match....
bio-vcf-manipulation
Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. I...
bio-variant-calling
Reference examples tested with: bcftools 1.19+ Before using code patterns, verify installed versions match. If versions ...
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 vers...
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 cod...
bio-tcr-bcr-analysis-repertoire-visualization
Reference examples tested with: MiXCR 4.6+, VDJtools 1.2.1+, ggplot2 3.5+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+, s...
bio-tcr-bcr-analysis-immcantation-analysis
Reference examples tested with: MiXCR 4.6+, ggplot2 3.5+ Before using code patterns, verify installed versions match. If...
bio-systems-biology-model-curation
pip install memote memote report snapshot model.xml --filename report.html memote run model.xml memote run --pytest-args...
bio-systems-biology-metabolic-reconstruction
pip install carveme carve genome.faa -o model.xml carve genome.faa -o model.xml --format sbml carve genome.faa -o model....
bio-systems-biology-gene-essentiality
import cobra from cobra.fluxanalysis import singlegenedeletion model = cobra.io.loadmodel('textbook') deletionresults = ...
bio-systems-biology-flux-balance-analysis
import cobra model = cobra.io.loadmodel('textbook') # E. coli core (95 reactions) model = cobra.io.loadmodel('iJO1366')...
bio-substructure-search
Reference examples tested with: RDKit 2024.03+ Before using code patterns, verify installed versions match. If versions ...
bio-structural-biology-modern-structure-prediction
Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match...
bio-structural-biology-alphafold-predictions
Reference examples tested with: BioPython 1.83+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+ Before using code patterns, ...