Neuro_SCpedia: an interactive tool for single cell sequencing data in neuroscience

Diplôme Master Neuro_SCpedia: an interactive tool for single cell sequencing data in neuroscience eng 2024-09 author Zhu Xintao 0009-0006-4040-9953 984162 director Jabaudon Denis 0000-0003-2438-4769 682473 Département de neurosciences fondamentales (NEUFO) 60 Nervous tissue is composed of highly heterogeneous types and subtypes of neurons. The advent of single-cell RNA sequencing (scRNA-seq) techniques has provided a way to extensively study the molecular identities and cellular diversity of nervous tissue at the single-cell level. This has led to the generation of large number of scRNA-seq datasets. However, accessing desired scRNA-seq datasets from the main public biodata repository “Gene Expression Omnibus” (GEO) remains challenging due to its complex and nonuniform searching interface. To promote the re-using and enhance retrieval accessibility of generated scRNA-seq datasets in the field of neuroscience, we developed a comprehensive and user-friendly Shiny App named “Neuro_SCpedia”. Using the NCBI’s web API tool “E-utilites” through R, we automatically compiled metadata of single-cell datasets related to neuroscience available in GEO. We then use “Neuro_SCpedia” (https://cmushiny.unige.ch/zhux/Neuro_SCpedia/) for statistical analysis to reveal trends in the technical development and application of scRNA-seq techniques in neuroscience. Finally, we created automated tools to display the data in Neuro_SCpedia to facilitate the use and analysis of these datas. We believe that this resource will significantly improve access to single-cell RNA sequencing data in the neuroscience field, promoting the reuse of existing data and facilitating meta-analyses. Dewey 616.8 Dewey 590 Maîtrise universitaire (Master) en Biologie 53 Département de neurosciences fondamentales 21A 44 Département de génétique et évolution 162 false 540 Neurobiologie développementale et plasticité 880 d3be5aa7-66e4-43d2-bb93-cc0e7a950ad9 Master thesis Restricted Xintao_ZHU_Master_Thesis_30082024.pdf 3587390 application/pdf 2b462f6cad2de34428315f6896dbc6e70411d81c17fe16e4536324c9f13f2642 restrictedAccess Faculté de médecine / Section de médecine fondamentale / Département de neurosciences fondamentales Faculté des sciences / Section de biologie / Département de génétique et évolution

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