Automates the end-to-end processing and curation of bulk RNA-seq datasets for VEuPathDB genomic resources.
This skill provides a comprehensive workflow for bioinformatics curators to process bulk RNA-seq datasets within the VEuPathDB ecosystem. It streamlines technical tasks such as fetching metadata from ENA, NCBI BioSample, and GEO, while offering advanced capabilities like extracting experimental context from journal PDFs via subagents. By guiding users through sample analysis, strandedness detection, and contact curation, it ensures the standardized generation of datasetPresenter XML and pipeline configuration files (samplesheets and analysis configs) required for backend data processing.
主な機能
01Automated generation of VEuPathDB-specific datasetPresenter XML
02Intelligent sample annotation and technical replicate grouping
03Standardized pipeline delivery outputs including samplesheet.csv and analysisConfig.xml
04Automated metadata retrieval from ENA and NCBI BioSample
050 GitHub stars
06Subagent-driven extraction of experimental details from journal PDFs
ユースケース
01Generating pipeline-ready configuration files for bioinformatics processing teams
02Integrating new RNA-seq BioProjects into VEuPathDB databases like ToxoDB or PlasmoDB
03Standardizing metadata for large-scale transcriptomic datasets
