SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Bioinformatics Année : 2017

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Résumé

Motivation: Flow, hyperspectral and mass cytometry are experimental techniques measuring cell marker expressions at the single cell level. The recent increase of the number of markers simultaneously measurable has led to the development of new automatic gating algorithms. Especially, the SPADE algorithm has been proposed as a novel way to identify clusters of cells having similar phenotypes in high-dimensional cytometry data. While SPADE or other cell clustering algorithms are powerful approaches, complementary analysis features are needed to better characterize the identified cell clusters. Results: We have developed SPADEVizR, an R package designed for the visualization, analysis and integration of cell clustering results. The available statistical methods allow highlighting cell clusters with relevant biological behaviors or integrating them with additional biological variables. Moreover, several visualization methods are available to better characterize the cell clusters, such as volcano plots, streamgraphs, parallel coordinates, heatmaps, or distograms. SPADEVizR can also generate linear, Cox or random forest models to predict biological outcomes, based on the cell cluster abundances. Additionally, SPADEVizR has several features allowing to quantify and to visualize the quality of the cell clustering results. These analysis features are essential to better interpret the behaviors and phenotypes of the identified cell clusters. Importantly, SPADEVizR can handle clustering results from other algorithms than SPADE.
Fichier principal
Vignette du fichier
Gautreau.pdf (573.46 Ko) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

hal-02385937 , version 1 (29-11-2019)

Identifiants

Citer

Guillaume Gautreau, David Pejoski, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon, et al.. SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results. Bioinformatics, 2017, pp.btw708. ⟨10.1093/bioinformatics/btw708⟩. ⟨hal-02385937⟩
80 Consultations
61 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More