Tag: bioinformatics
CUT and CUT Processing Pipeline
Executes a Nextflow-based pipeline for processing CUT and CUT data from FASTQ files to peaks and signal tracks. The workflow incorporates spike-in normalisation and SEACR peak calling for high-resolution chromatin profiling.
DNase-seq pipeline for accessibility and footprints
Executes a comprehensive DNase-seq workflow, processing paired-end FASTQ reads to identify DNase hypersensitive sites (DHSs) and perform transcription factor footprinting. The pipeline leverages Nextflow to manage alignment, peak calling vi…
ENCODE ChIP-seq Processing Pipeline
This Nextflow-based pipeline executes the complete ENCODE ChIP-seq processing workflow, transforming raw FASTQ files into peaks and signal tracks. It handles quality control, alignment, peak calling with MACS2, and IDR analysis using Docker…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility
This tool executes the full ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and rigorous filtering. It generates nucleosome-free peaks and signal tracks following established ENCODE standards.
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…
genomic coordinate liftover workflow guide
This skill provides a definitive workflow for safely converting genomic coordinates between different assembly versions (e.g., hg19 to hg38). It guides the use of industry-standard tools like UCSC liftOver and CrossMap, ensuring full proven…
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…
Aggregate Hi-C Chromatin Contact Maps
Aggregates BEDPE loop calls from multiple ENCODE Hi-C experiments to create a comprehensive union catalog of chromatin contacts. It performs resolution-aware anchor matching, quality-gating, and filtering against the ENCODE blacklist.
Integrating GTEx Expression with ENCODE Data
This skill enables the integration of GTEx tissue expression data with ENCODE regulatory elements to validate enhancer-gene links and assess tissue-specific activity. It facilitates querying median TPM, eQTLs, and transcript-level expressio…
NCBI GEO and ENCODE Data Connector
Search, query, and cross-reference NCBI GEO datasets with ENCODE experiments to identify complementary genomic data. The skill facilitates downloading metadata, series matrices, and supplementary files while enabling the linking of GEO acce…
Ensembl Genomic Annotation and VEP Skill
Query the Ensembl REST API to perform variant effect prediction (VEP), coordinate liftover between assemblies, and retrieve regulatory feature annotations. The skill also facilitates gene identifier resolution and phenotype association look…
ENCODE Genomics Data Downloader and Manager
This tool facilitates the programmatic retrieval of diverse ENCODE genomics files, supporting both specific accession downloads and comprehensive batch operations. It includes advanced features such as dry-run previews, MD5 verification, an…
Disease Research with ENCODE Functional Genomics
This skill enables researchers to investigate disease mechanisms by connecting GWAS variants to ENCODE regulatory elements and functional genomics data. It integrates ENCODE annotations with Open Targets, PubMed, and ClinicalTrials.gov to i…
Comparing ENCODE Experiments Across Biosamples
This skill enables the systematic comparison of ENCODE experiments across various tissues, cell lines, and biosamples to identify tissue-specific regulatory patterns. It facilitates the identification of constitutive versus variable regulat…
Cross-reference ENCODE data with scientific databases
This skill facilitates the comprehensive cross-referencing of ENCODE genomic data with major external scientific resources. It enables the construction of translational pipelines by linking experiments to literature, clinical trials, and va…
Resolving ENCODE Bulk Signals with CellxGene
This skill enables the integration of CellxGene Census single-cell RNA-seq data with bulk ENCODE functional genomics experiments to resolve cell-type-specific regulatory activity. It facilitates the deconvolution of bulk signals and the val…
Setup reproducible bioinformatics environments for ENCODE
This skill provisions fully reproducible, version-pinned computational environments for diverse ENCODE assays, generating conda definitions, R/Bioconductor scripts, and Python requirements. It simplifies the setup of complex pipelines (e.g.…
Systematic ENCODE Experiment Batch Processing
Facilitates systematic batch operations across multiple ENCODE experiments, including quality control screening, bulk downloading, and comparative analysis. It provides workflows for managing large-scale data collections and generating summ…
Aggregate Chromatin Accessibility Peaks Across Studies
This skill generates a comprehensive union map of open chromatin by merging ATAC-seq and DNase-seq narrowPeak data from multiple ENCODE experiments. It handles cross-platform variation and applies rigorous filtering and confidence annotatio…