دورية أكاديمية
scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data.
| العنوان: | scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data. |
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| المؤلفون: | Lepetit M; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France., Ilie MD; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France.; Endocrinology Department, 'C.I.Parhon' National Institute of Endocrinology, Bucharest, Romania., Chanal M; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France., Raverot G; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France.; Endocrinology Department, Reference Center for Rare Pituitary Diseases HYPO, 'Groupement Hospitalier Est' Hospices Civils de Lyon, Bron, France., Bertolino P; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France., Arpin C; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France., Picard F; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France., Gandrillon O; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France.; Inria Center Grenoble Rhone-Alpes, Equipe Dracula, Villeurbanne, France. |
| المصدر: | In silico biology [In Silico Biol] 2023; Vol. 15 (1-2), pp. 11-21. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9815902 Publication Model: Print Cited Medium: Internet ISSN: 1434-3207 (Electronic) Linking ISSN: 13866338 NLM ISO Abbreviation: In Silico Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Amsterdam ; Washington, DC : [Tokyo] : IOS Press ; Ohmsha, c1998- |
| مواضيع طبية MeSH: | RNA-Seq* , Single-Cell Gene Expression Analysis* , Software*, Datasets as Topic ; Humans ; Animals ; Mice ; Pituitary Neoplasms/genetics ; CD8-Positive T-Lymphocytes ; Gene Expression Profiling ; Computational Biology ; Workflow |
| مستخلص: | Single cell transcriptomics has recently seen a surge in popularity, leading to the need for data analysis pipelines that are reproducible, modular, and interoperable across different systems and institutions.To meet this demand, we introduce scAN1.0, a processing pipeline for analyzing 10X single cell RNA sequencing data. scAN1.0 is built using the Nextflow DSL2 and can be run on most computational systems. The modular design of Nextflow pipelines enables easy integration and evaluation of different blocks for specific analysis steps.We demonstrate the usefulness of scAN1.0 by showing its ability to examine the impact of the mapping step during the analysis of two datasets: (i) a 10X scRNAseq of a human pituitary gonadotroph tumor dataset and (ii) a murine 10X scRNAseq acquired on CD8 T cells during an immune response. |
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| فهرسة مساهمة: | Keywords: Pipeline; annotation; data analysis; mapping; single cell transcriptomics |
| تواريخ الأحداث: | Date Created: 20231106 Date Completed: 20231122 Latest Revision: 20231224 |
| رمز التحديث: | 20231224 |
| مُعرف محوري في PubMed: | PMC10741331 |
| DOI: | 10.3233/ISB-220252 |
| PMID: | 37927254 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1434-3207 |
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| DOI: | 10.3233/ISB-220252 |