Search ENCODE Project experiments and datasets by assay, organism, and tissue.
npx skills add https://github.com/ammawla/encode-toolkit --skill search-encode
Please help me install this Agent Skill. Skill: search-encode Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/search-encode Command: npx skills add https://github.com/ammawla/encode-toolkit --skill search-encode
This Skill enables users to locate and explore ENCODE Project genomic datasets with precision, saving time and reducing search errors.
Start by exploring available assays in a specific tissue and then refine your search to find relevant experiments and files.
High-intent search queries and answers about installing and using this skill.
You can discover ENCODE genomic datasets by applying structured filters for assay type, organism, tissue, and targets. This facilitates precise, metadata-driven retrieval of relevant experiments and their associated files.
Yes, you can retrieve analysis-ready files and specific experiment metadata from the ENCODE Project. The Skill enables detailed retrieval of experimental parameters and data files optimized for downstream genomic analysis.
The best way to explore genomic assays in a specific organ is through faceted exploration. You can preview data availability using filters like biosample type, assay, and organ to guide targeted searches.
Yes, filtering ENCODE data by biosample type and target is fully supported. You can perform faceted exploration across multiple assay types and biosamples to ensure relevant, scalable search results.
To locate high-quality human liver ChIP-seq peak files in ENCODE, search by tissue and assay, then refine results by quality parameters. This retrieves visualization-ready peak files and associated metadata for downstream analysis.
hxk622Read, write, and manipulate genomic data files via htslib.
ovachieverConvert BAM alignments into normalized coverage tracks and generate QC metrics.
AlterLab-IEUQuery Ensembl REST API for genes, sequences, variants, and orthologs.
ammawlaSearch GEO datasets and link them to ENCODE experiments via NCBI E-utilities.
