Tag: encode
Annotating Genetic Variants with ENCODE Data
Annotate genetic variants with ENCODE functional genomics data to identify causal regulatory elements and link them to target genes. The skill supports the full post-GWAS workflow, including tissue-specific mapping, enrichment testing, and …
Analyzing ENCODE single-cell genomics data
This skill guides the retrieval and analysis of single-cell genomics data (scRNA-seq and scATAC-seq) from the ENCODE project. It provides detailed protocols for data structure, quality assessment, and integrating single-cell profiles with b…
Search and explore ENCODE genomics data
This skill facilitates comprehensive querying and exploration of the ENCODE Project's vast genomics dataset. It guides users through a structured, multi-phase search process, allowing them to first explore available facets, validate metadat…
Characterize Genomic Regulatory Elements Using ENCODE Data
This skill facilitates the discovery and classification of cis-regulatory elements (cCREs) by integrating ENCODE's comprehensive catalog with multi-omic data. It supports advanced analysis of chromatin states, identifying promoters, enhance…
Comprehensive ENCODE Data Quality Assessment Skill
This skill evaluates the reliability of ENCODE experiments by interpreting multiple orthogonal quality metrics, such as FRiP, NSC, and NRF, alongside official audit flags. It provides deep guidance for filtering and comparing data across va…
ENCODE ChIP-seq Analysis Pipeline for Peak Calling
This skill executes a complete, standards-compliant ChIP-seq workflow, processing raw FASTQ files through alignment, MACS2 peak calling, and IDR analysis. It generates comprehensive peak sets and signal tracks, adhering to ENCODE guidelines…
ENCODE Multi-Omics Data Integration
Integrates multiple ENCODE data types, including RNA-seq, ATAC-seq, and ChIP-seq, to construct a comprehensive regulatory landscape for specific tissues or cell types. It enables chromatin state annotation, enhancer-gene linkage, and the ch…
Aggregate DNA Methylation Data Across Studies
Construct comprehensive tissue-level DNA methylation landscapes by aggregating WGBS data from multiple ENCODE experiments. The process includes quality-gating, coverage filtering, and the identification of hypomethylated regions and partial…
ENCODE Multi-omic Data Integration
Provides a framework for planning and executing integrative analyses across multiple ENCODE experiments, including multi-omic and cross-sample workflows. It assists with compatibility verification, integration strategy selection, and the re…
gwas-encode integration for functional variant annotation
This skill facilitates the intersection of genome-wide association study variants with ENCODE's functional regulatory elements. It helps developers prioritise candidate causal mechanisms by identifying which disease-associated SNPs overlap …
NCBI GEO and ENCODE Connector
Facilitates searching, querying, and cross-referencing NCBI GEO datasets with ENCODE experiments to identify complementary epigenomic data. It supports retrieving metadata, series matrices, and supplementary files via E-utilities and FTP.
Validate Regulatory Elements with GTEx Expression
This skill facilitates the integration of GTEx tissue expression data with ENCODE regulatory element findings, allowing developers to validate enhancer-gene links and assess tissue-specific gene activity. It enables the correlation of predi…
Comprehensive Epigenomic Profiling with ENCODE
Assemble comprehensive epigenomic profiles for specific tissues or cell types by systematically gathering histone modifications, chromatin accessibility, and DNA methylation data from ENCODE. It enables the characterisation of chromatin sta…
Cross-reference ENCODE with scientific databases
Link ENCODE genomic data to external scientific databases such as PubMed, ClinicalTrials.gov, and Open Targets. This skill facilitates building translational pipelines by connecting regulatory elements to clinical research and variant annot…
Annotating ENCODE Regulatory Variants with ClinVar
Cross-reference ENCODE functional genomic elements with ClinVar clinical variant classifications to identify pathogenic variants in regulatory regions. This skill enables both forward annotation of ENCODE peaks and reverse analysis of ClinV…
Setup reproducible bioinformatics environments for ENCODE
This skill provisions fully reproducible, version-pinned conda environments and associated scripts for comprehensive ENCODE data analysis. It manages dependencies across multiple modalities (RNA-seq, ChIP-seq, ATAC-seq) using tools like STA…
annotate non-coding variants using encode data
This skill interprets non-coding genetic variation by layering ENCODE functional genomics annotations (e.g., cCREs, enhancers) onto variant sets. It supports the full post-GWAS workflow, including tissue-specific mapping, fine-mapping, and …
ENCODE Single-Cell Genomics Data Analysis Guide
This skill guides the retrieval and analysis of single-cell genomics data (scRNA-seq and scATAC-seq) from ENCODE. It covers data structure, quality control metrics, and best practices for integrating single-cell profiles with bulk epigenomi…
Configure and connect to ENCODE Project data
This skill guides users through the installation, configuration, and authentication process for the ENCODE Toolkit MCP server. It ensures the local environment is correctly connected to the ENCODE Project genomics database for subsequent da…
Characterise Regulatory Elements with ENCODE Data
Identify and characterise candidate cis-regulatory elements using ENCODE datasets and the cCRE catalog. The skill enables the discovery of active enhancers, promoter state mapping, and super-enhancer identification using ChromHMM and ROSE.
Generate scientific text from ENCODE provenance
This skill auto-generates publication-ready scientific documentation, including methods sections and figure legends, by rigorously compiling experimental and computational metadata from ENCODE provenance records. It ensures adherence to hig…
ENCODE Pipeline Workflow Generation and Management
This skill facilitates the generation and execution of complex ENCODE bioinformatics workflows, supporting custom Nextflow and WDL pipelines. It manages compute resource requirements and deployment across local, HPC, and major cloud platfor…
Aggregate DNA Methylation Across ENCODE Studies
Build comprehensive tissue-level DNA methylation landscapes by aggregating WGBS data from multiple ENCODE experiments. The skill handles quality-gating, coverage filtering, and the identification of hypomethylated regions and partially meth…
Integrating JASPAR Motifs with ENCODE ChIP-seq
Integrate JASPAR transcription factor binding profiles with ENCODE ChIP-seq peaks to validate binding targets and discover co-factors. This skill enables scanning regulatory regions for motif enrichment and assessing the impact of genomic v…