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CrossTalkeR: analysis and visualization of ligand–receptorne tworks

Nagai, James S ; Leimkühler, Nils B ; Schaub, Michael T ; Schneider, Rebekka K ; Costa, Ivan G Mathelier, Anthony

Bioinformatics (Oxford, England), 2021-11, Vol.37 (22), p.4263-4265 [Periódico revisado por pares]

England: Oxford University Press

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  • Título:
    CrossTalkeR: analysis and visualization of ligand–receptorne tworks
  • Autor: Nagai, James S ; Leimkühler, Nils B ; Schaub, Michael T ; Schneider, Rebekka K ; Costa, Ivan G
  • Mathelier, Anthony
  • Assuntos: Applications Notes ; Gene Expression Profiling ; Humans ; Ligands ; Sequence Analysis, RNA ; Single-Cell Analysis ; Software
  • É parte de: Bioinformatics (Oxford, England), 2021-11, Vol.37 (22), p.4263-4265
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
  • Descrição: Abstract Motivation Ligand–receptor (LR) network analysis allows the characterization of cellular crosstalk based on single cell RNA-seq data. However, current methods typically provide a list of inferred LR interactions and do not allow the researcher to focus on specific cell types, ligands or receptors. In addition, most of these methods cannot quantify changes in crosstalk between two biological phenotypes. Results CrossTalkeR is a framework for network analysis and visualization of LR interactions. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological phenotypes, i.e. disease versus homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterization of changes in cellular crosstalk in disease. Availability and implementation CrosstalkeR is an R package available at: Github: https://github.com/CostaLab/CrossTalkeR. Supplementary information Supplementary data are available at Bioinformatics online.
  • Editor: England: Oxford University Press
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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