Nextflow pipeline for Visium and H&E data from patient-derived xenograft samples DOI Creative Commons
Sergii Domanskyi, Anuj Srivastava, Jessica Kaster

и другие.

Cell Reports Methods, Год журнала: 2024, Номер 4(5), С. 100759 - 100759

Опубликована: Апрель 15, 2024

We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and matched hematoxylin eosin (H&E)-stained whole-slide image (WSI), optimized patient-derived xenograft (PDX) cancer specimens. Our pipeline enables the classification sequenced transcripts deconvolving mouse human species mapping to reference transcriptomes. align H&E WSI with layout slide generate imaging quantitative morphology features each spot. The design multiple analysis workflows, including single or dual genome input stand-alone analysis. show utility our on dataset from profiling four melanoma PDX samples. clustering spots reveal similar patterns arising two modalities.

Язык: Английский

Nextflow pipeline for Visium and H&E data from patient-derived xenograft samples DOI Creative Commons
Sergii Domanskyi, Anuj Srivastava, Jessica Kaster

и другие.

Cell Reports Methods, Год журнала: 2024, Номер 4(5), С. 100759 - 100759

Опубликована: Апрель 15, 2024

We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and matched hematoxylin eosin (H&E)-stained whole-slide image (WSI), optimized patient-derived xenograft (PDX) cancer specimens. Our pipeline enables the classification sequenced transcripts deconvolving mouse human species mapping to reference transcriptomes. align H&E WSI with layout slide generate imaging quantitative morphology features each spot. The design multiple analysis workflows, including single or dual genome input stand-alone analysis. show utility our on dataset from profiling four melanoma PDX samples. clustering spots reveal similar patterns arising two modalities.

Язык: Английский

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