ammawla/encode-toolkit

ammawla/encode-toolkit · plugin/skills/accessibility-aggregation/SKILL.md · Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple…

ammawla/encode-toolkit · plugin/skills/batch-analysis/SKILL.md · Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across…

ammawla/encode-toolkit · plugin/skills/bioinformatics-installer/SKILL.md · Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor…

ammawla/encode-toolkit · plugin/skills/cellxgene-context/SKILL.md · Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need…

ammawla/encode-toolkit · plugin/skills/cite-encode/SKILL.md · Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE…

ammawla/encode-toolkit · plugin/skills/clinvar-annotation/SKILL.md · Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if…

ammawla/encode-toolkit · plugin/skills/compare-biosamples/SKILL.md · Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory…

ammawla/encode-toolkit · plugin/skills/cross-reference/SKILL.md · Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog…

ammawla/encode-toolkit · plugin/skills/data-provenance/SKILL.md · Track exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and…

ammawla/encode-toolkit · plugin/skills/disease-research/SKILL.md · Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to…

ammawla/encode-toolkit · plugin/skills/download-encode/SKILL.md · Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to…

ammawla/encode-toolkit · plugin/skills/ensembl-annotation/SKILL.md · Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover…

ammawla/encode-toolkit · plugin/skills/epigenome-profiling/SKILL.md · Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to…

ammawla/encode-toolkit · plugin/skills/functional-screen-analysis/SKILL.md · Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and…

ammawla/encode-toolkit · plugin/skills/geo-connector/SKILL.md · Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the…

ammawla/encode-toolkit · plugin/skills/gnomad-variants/SKILL.md · Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant…

ammawla/encode-toolkit · plugin/skills/gtex-expression/SKILL.md · Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a…

ammawla/encode-toolkit · plugin/skills/gwas-catalog/SKILL.md · Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS…

ammawla/encode-toolkit · plugin/skills/hic-aggregation/SKILL.md · Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments…

ammawla/encode-toolkit · plugin/skills/histone-aggregation/SKILL.md · Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and…

ammawla/encode-toolkit · plugin/skills/integrative-analysis/SKILL.md · Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows…

ammawla/encode-toolkit · plugin/skills/jaspar-motifs/SKILL.md · Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF…

ammawla/encode-toolkit · plugin/skills/liftover-coordinates/SKILL.md · Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver…

ammawla/encode-toolkit · plugin/skills/methylation-aggregation/SKILL.md · Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple…

ammawla/encode-toolkit · plugin/skills/motif-analysis/SKILL.md · Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite…

ammawla/encode-toolkit · plugin/skills/multi-omics-integration/SKILL.md · Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build…

ammawla/encode-toolkit · plugin/skills/peak-annotation/SKILL.md · Guide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT. Use when users need to assign peaks…

ammawla/encode-toolkit · plugin/skills/pipeline-atacseq/SKILL.md · Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides…

ammawla/encode-toolkit · plugin/skills/pipeline-chipseq/SKILL.md · Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides…

ammawla/encode-toolkit · plugin/skills/pipeline-cutandrun/SKILL.md · Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow…

ammawla/encode-toolkit · plugin/skills/pipeline-dnaseseq/SKILL.md · Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints. Child of pipeline-guide. Provides Nextflow…

ammawla/encode-toolkit · plugin/skills/pipeline-guide/SKILL.md · Access ENCODE uniform analysis pipelines, generate user-specific Nextflow/WDL pipelines, manage compute resources, and…

ammawla/encode-toolkit · plugin/skills/pipeline-hic/SKILL.md · Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow…

ammawla/encode-toolkit · plugin/skills/pipeline-rnaseq/SKILL.md · Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides…

ammawla/encode-toolkit · plugin/skills/pipeline-wgbs/SKILL.md · Execute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of…

ammawla/encode-toolkit · plugin/skills/publication-trust/SKILL.md · Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill…

ammawla/encode-toolkit · plugin/skills/quality-assessment/SKILL.md · Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality…

ammawla/encode-toolkit · plugin/skills/regulatory-elements/SKILL.md · Discover and characterize regulatory elements (enhancers, promoters, silencers, insulators, super-enhancers) using…

ammawla/encode-toolkit · plugin/skills/scientific-writing/SKILL.md · Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements…

ammawla/encode-toolkit · plugin/skills/scrna-meta-analysis/SKILL.md · Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell…

ammawla/encode-toolkit · plugin/skills/search-encode/SKILL.md · Search and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what…

ammawla/encode-toolkit · plugin/skills/setup/SKILL.md · Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting…

ammawla/encode-toolkit · plugin/skills/single-cell-encode/SKILL.md · Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about…

ammawla/encode-toolkit · plugin/skills/track-experiments/SKILL.md · Track ENCODE experiments locally with publications, citations, and provenance. Use when the user wants to build a…

ammawla/encode-toolkit · plugin/skills/ucsc-browser/SKILL.md · Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding…

ammawla/encode-toolkit · plugin/skills/variant-annotation/SKILL.md · Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding…

ammawla/encode-toolkit · plugin/skills/visualization-workflow/SKILL.md · Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and…

ammawla/encode-toolkit · skills/accessibility-aggregation/SKILL.md · Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple…

ammawla/encode-toolkit · skills/batch-analysis/SKILL.md · Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across…

ammawla/encode-toolkit · skills/bioinformatics-installer/SKILL.md · Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor…

ammawla/encode-toolkit · skills/cellxgene-context/SKILL.md · Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need…

ammawla/encode-toolkit · skills/cite-encode/SKILL.md · Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE…

ammawla/encode-toolkit · skills/clinvar-annotation/SKILL.md · Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if…

ammawla/encode-toolkit · skills/compare-biosamples/SKILL.md · Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory…

ammawla/encode-toolkit · skills/cross-reference/SKILL.md · Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog…

ammawla/encode-toolkit · skills/data-provenance/SKILL.md · Track exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and…

ammawla/encode-toolkit · skills/disease-research/SKILL.md · Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to…

ammawla/encode-toolkit · skills/download-encode/SKILL.md · Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to…

ammawla/encode-toolkit · skills/ensembl-annotation/SKILL.md · Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover…

ammawla/encode-toolkit · skills/epigenome-profiling/SKILL.md · Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to…

ammawla/encode-toolkit · skills/functional-screen-analysis/SKILL.md · Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and…

ammawla/encode-toolkit · skills/geo-connector/SKILL.md · Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the…

ammawla/encode-toolkit · skills/gnomad-variants/SKILL.md · Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant…

ammawla/encode-toolkit · skills/gtex-expression/SKILL.md · Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a…

ammawla/encode-toolkit · skills/gwas-catalog/SKILL.md · Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS…

ammawla/encode-toolkit · skills/hic-aggregation/SKILL.md · Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments…

ammawla/encode-toolkit · skills/histone-aggregation/SKILL.md · Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and…

ammawla/encode-toolkit · skills/integrative-analysis/SKILL.md · Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows…

ammawla/encode-toolkit · skills/jaspar-motifs/SKILL.md · Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF…

ammawla/encode-toolkit · skills/liftover-coordinates/SKILL.md · Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver…

ammawla/encode-toolkit · skills/methylation-aggregation/SKILL.md · Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple…

ammawla/encode-toolkit · skills/motif-analysis/SKILL.md · Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite…

ammawla/encode-toolkit · skills/multi-omics-integration/SKILL.md · Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build…