ammawla/encode-toolkit
47 skills
$npx skills add ammawla/encode-toolkitSkillInstalls
accessibility-aggregationBuild comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs.batch-analysisGuide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously.bioinformatics-installerInstall bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker),…cellxgene-contextGuide for integrating CellxGene Census single-cell data with ENCODE bulk experiments.cite-encodeGenerate proper ENCODE citations for publications, grants, and presentations.clinvar-annotationGuide for annotating ENCODE regulatory variants with ClinVar clinical significance.compare-biosamplesCompare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns.cross-referenceCross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific…data-provenanceTrack exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and timestamps — to enable publication-ready…disease-researchUse ENCODE functional genomics data for disease mechanism research.download-encodeDownload ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.ensembl-annotationQuery the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references.epigenome-profilingBuild comprehensive epigenomic profiles for tissues or cell types using ENCODE data.functional-screen-analysisAnalyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq.geo-connectorSearch, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments.gnomad-variantsQuery gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory…gtex-expressionGuide for integrating GTEx tissue expression data with ENCODE regulatory elements.gwas-catalogGuide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data.hic-aggregationBuild comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs.histone-aggregationBuild comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs.integrative-analysisPlan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows.jaspar-motifsGuide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data.liftover-coordinatesConvert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10).methylation-aggregationBuild comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs.motif-analysisGuide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite.multi-omics-integrationIntegrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape.peak-annotationGuide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT.pipeline-atacseqExecute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide.pipeline-chipseqExecute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide.pipeline-cutandrunExecute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide.pipeline-dnaseseqExecute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment.pipeline-guideAccess ENCODE uniform analysis pipelines, generate user-specific Nextflow/WDL pipelines, manage compute resources, and integrate with cloud platforms.pipeline-hicExecute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide.pipeline-rnaseqExecute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide.pipeline-wgbsExecute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of pipeline-guide.publication-trustAssess the scientific integrity and trustworthiness of publications before relying on their findings.quality-assessmentEvaluate ENCODE experiment quality using standard metrics and audit flags.regulatory-elementsDiscover and characterize regulatory elements (enhancers, promoters, silencers, insulators, super-enhancers) using ENCODE data and the cCRE catalog.scientific-writingGenerate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance.scrna-meta-analysisConduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type.search-encodeSearch and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what data is available for specific assays,…setupSet up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.single-cell-encodeFind and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq.track-experimentsTrack ENCODE experiments locally with publications, citations, and provenance.ucsc-browserQuery the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic…variant-annotationAnnotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation.visualization-workflowComprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots.