Repository logo
 
Publication

MigraR: An open-source, R-based application for analysis and quantification of cell migration parameters

2022-01Journal article Restricted access
Simple item page
dc.contributor.authorShaji, Nirbhaya
dc.contributor.authorNunes, Florbela
dc.contributor.authorRocha, M Ines
dc.contributor.authorGomes, Elsa Ferreira
dc.contributor.authorCastro, Helena
dc.date.accessioned2023-02-06T09:23:42Z
dc.date.embargo2035-12-15
dc.date.issued2022-01
dc.description.abstractCell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell trajectories recorded by time-lapse video microscopy. Dedicated software tools exist to assist the automated or semi-automated tracking of cells and translate these into coordinate positions along time. However, cell biologists usually bump into the difficulty of plotting and computing these data sets into biologically meaningful figures and metrics. Methods: This report describes MigraR, an intuitive graphical user interface executed from the RStudioTM (via the R package Shiny), which greatly simplifies the task of translating coordinate positions of moving cells into measurable parameters of cell migration (velocity, straightness, and direction of movement), as well as of plotting cell trajectories and migration metrics. One innovative function of this interface is that it allows users to refine their data sets by setting limits based on time, velocity and straightness. Results: MigraR was tested on different data to assess its applicability. Intended users of MigraR are cell biologists with no prior knowledge of data analysis, seeking to accelerate the quantification and visualization of cell migration data sets delivered in the format of Excel files by available cell-tracking software. Conclusions: Through the graphics it provides, MigraR is an useful tool for the analysis of migration parameters and cellular trajectories. Since its source code is open, it can be subject of refinement by expert users to best suit the needs of other researchers. It is available at GitHub and can be easily reproduced.pt_PT
dc.description.sponsorshipThis work is financed by National Funds through the Portuguese funding agency, FCT- Fundação para a Ciência e a Tecnologia, within project UIDB/50014/2020.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1016/j.cmpb.2021.106529pt_PT
dc.identifier.urihttp://hdl.handle.net/10400.22/22151
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherElsevierpt_PT
dc.relationINESC TEC- Institute for Systems and Computer Engineering, Technology and Science
dc.relation.publisherversionhttps://www.sciencedirect.com/science/article/pii/S0169260721006039?via%3Dihubpt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/pt_PT
dc.subjectShiny applicationpt_PT
dc.subjectCell-tracking softwarept_PT
dc.subjectVisualizationpt_PT
dc.subjectR languagept_PT
dc.titleMigraR: An open-source, R-based application for analysis and quantification of cell migration parameterspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleINESC TEC- Institute for Systems and Computer Engineering, Technology and Science
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F50014%2F2020/PT
oaire.citation.issue106529pt_PT
oaire.citation.titleComputer Methods and Programs in Biomedicinept_PT
oaire.citation.volume213pt_PT
oaire.fundingStream6817 - DCRRNI ID
person.familyNameGomes
person.givenNameElsa
person.identifierR-000-4K3
person.identifier.ciencia-id7613-615A-3DEA
person.identifier.orcid0000-0003-3610-8788
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsclosedAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublicationf43a41aa-1505-4416-b6ef-709422c5c2c9
relation.isAuthorOfPublication.latestForDiscoveryf43a41aa-1505-4416-b6ef-709422c5c2c9
relation.isProjectOfPublication7a2d9a82-ee07-4c57-bbbf-2d88b942688d
relation.isProjectOfPublication.latestForDiscovery7a2d9a82-ee07-4c57-bbbf-2d88b942688d

Files

Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
1-s2.0-S0169260721006039-main.pdf
Size:
2.09 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

ISEP – DEI – Artigos