CERTOMICS is a Nextflow-based pipeline offering enhanced CERTainty in immunophenotyping and data interpretation, tailored for single-cell multiOMICS profiling of adoptive cellular immunotherapies. The pipeline standardises processing 10x Genomics single-cell multiomics data and integrates CAR-specific identification and quality control. Additionally, a curated repository of CAR construct sequences and annotation data is provided, serving as a resource to support the analysis and development of CAR T cell therapies.
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