Package: cellmigRation 1.15.0

Waldir Leoncio

cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.

Authors:Salim Ghannoum [aut, cph], Damiano Fantini [aut, cph], Waldir Leoncio [cre, aut], Øystein Sørensen [aut]

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cellmigRation.pdf |cellmigRation.html✨
cellmigRation/json (API)
NEWS

# Install 'cellmigRation' in R:

install.packages('cellmigRation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ocbe-uio/cellmigration/issues

Datasets:

TrajectoryDataset - Trajectories of 350 cells

On BioConductor:cellmigRation-1.15.0(bioc 3.21)cellmigRation-1.14.0(bioc 3.20)

cellbiology datarepresentation dataimport bioconductor-package cell-tracking shiny trajectory-analysis

4.60 score 4 scripts 130 downloads 67 exports 129 dependencies

Last updated 2 months agofrom:16757c864e. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	OK	Nov 29 2024
R-4.3-mac	OK	Nov 29 2024

Exports:aggregateFR aggregateTrackedCells CellMig CellMigPCA CellMigPCAclust CellMigPCAclustALL CellTracker ComputeTracksStats DiAutoCor DiRatio DiRatioPlot EstimateDiameterRange FilterTrackedCells FinRes FMI ForwardMigration getAvailableAggrMetrics getCellImages getCellMigSlot getCellsMeta getCellsStats getCellTrackMeta getCellTracks getCellTrackStats getDACtable getDiRatio getFMItable getForMigtable getImageCentroids getImageStacks getMSDtable getOptimizedParameters getOptimizedParams getPerAndSpeed getPopulationStats getProcessedImages getProcessingStatus getResults getTracks getVACtable LoadTiff MSD OptimizeParams PerAndSpeed plot3DAllTracks plot3DTracks plotAllTracks plotSampleTracks PlotTracksSeparately rmPreProcessing setAnalyticParams setCellMigSlot setCellsMeta setCellTracks setExpName setOptimizedParams setProcessedImages setProcessingStatus setTrackedCellsMeta setTrackedCentroids setTrackedPositions setTrackingStats VeAutoCor visualizeCellTracks VisualizeImg VisualizeStackCentroids wsaPreProcessing

Dependencies:abind backports base64enc boot broom bslib cachem car carData checkmate cli cluster coda codetools colorspace cowplot cpp11 crosstalk data.table Deriv deSolve digest doBy doParallel dplyr DT ellipse emmeans estimability evaluate FactoMineR fansi farver fastmap flashClust FME fontawesome foreach foreign Formula fs generics ggplot2 ggrepel glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httpuv isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval leaps lifecycle lme4 magic magrittr MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime minpack.lm minqa modelr multcompView munsell mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plyr promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang rmarkdown rootSolve rpart rstudioapi sass scales scatterplot3d sm sp SparseM SpatialTools spBayes stringi stringr survival tibble tidyr tidyselect tiff tinytex utf8 vctrs vioplot viridis viridisLite withr xfun yaml zoo

cellmigRation

Rendered fromcellmigRation.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-03-19
Started: 2021-03-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregating the outcome of several experiments or conditions.	aggregateFR
Aggregate trackedCells Objects	aggregateTrackedCells
The CellMig Class.	CellMig CellMig-class initialize,CellMig-method
PCA	CellMigPCA
PCA Clusters	CellMigPCAclust
PCA Clusters of different conditions	CellMigPCAclustALL
Compute Cell Tracks	CellTracker
Compute Tracks Stats	ComputeTracksStats
Direction AutoCorrelation	DiAutoCor
Directionality Table	DiRatio
Directionality Ratio plots	DiRatioPlot
Detect Paricle Diameters in a Numeric matrix	EstimateDiameterRange
Filter an Aggregated Table of Cell Tracks	FilterTrackedCells
Final Results	FinRes
Forward Migration Index	FMI
Forward Migration	ForwardMigration
Get Available Aggregate Cell Metrics	getAvailableAggrMetrics
Method getCellImages	getCellImages getCellImages,trackedCells-method
Method getCellMigSlot	getCellMigSlot getCellMigSlot,CellMig,character-method
Get MetaData	getCellsMeta
Get Cell migration stats	getCellsStats
Method getCellTrackMeta	getCellTrackMeta getCellTrackMeta,trackedCells-method
Method getCellTracks	getCellTracks getCellTracks,trackedCells-method
Method getCellTrackStats	getCellTrackStats getCellTrackStats,trackedCells-method
Getting the Direction AutoCorrelation	getDACtable
Getting the Directionality Table	getDiRatio
Getting the Forward Migration Index	getFMItable
Getting the Forward Migration	getForMigtable
Method getImageCentroids	getImageCentroids getImageCentroids,trackedCells-method
Get Image Stacks	getImageStacks
Getting the Mean Square Displacement	getMSDtable
Get Auto Optimized Parameters	getOptimizedParameters
Method getOptimizedParams	getOptimizedParams getOptimizedParams,trackedCells-method
Getting the table of Persistence and Speed.	getPerAndSpeed
Get Cell population stats	getPopulationStats
Method getProcessedImages	getProcessedImages getProcessedImages,trackedCells-method
Method getProcessingStatus	getProcessingStatus getProcessingStatus,trackedCells-method
Final Results	getResults
Get Track Data	getTracks
Getting the Velocity AutoCorrelation	getVACtable
Import Image from TIFF	LoadTiff
Mean Square Displacement	MSD
Optimize Detection Params	OptimizeParams
Persistence and Speed	PerAndSpeed
A 3D rose-plot of all cells	plot3DAllTracks
A 3D rose-plot	plot3DTracks
A 2D rose-plot	plotAllTracks
A 2D rose-plot of sample cells	plotSampleTracks
A graphical display of the track of each cell.	PlotTracksSeparately
Data preprocessing for random migration (RM)	rmPreProcessing
Method setAnalyticParams	setAnalyticParams setAnalyticParams,trackedCells,list-method
Method setCellMigSlot	setCellMigSlot setCellMigSlot,CellMig,character,ANY-method setCellMigSlot,CellMig,character-method
Set MetaData	setCellsMeta
Method setCellTracks	setCellTracks setCellTracks,trackedCells,matrix-method
Method setExpName	setExpName setExpName,CellMig,character-method
Method setOptimizedParams	setOptimizedParams setOptimizedParams,trackedCells,ANY,ANY-method setOptimizedParams,trackedCells-method
Method setProcessedImages	setProcessedImages setProcessedImages,trackedCells,list-method
Method setProcessingStatus	setProcessingStatus setProcessingStatus,trackedCells,character,numeric-method
Method setTrackedCellsMeta	setTrackedCellsMeta setTrackedCellsMeta,trackedCells,list-method
Method setTrackedCentroids	setTrackedCentroids setTrackedCentroids,trackedCells,list-method
Method setTrackedPositions	setTrackedPositions setTrackedPositions,trackedCells,data.frame-method
Method setTrackingStats	setTrackingStats setTrackingStats,trackedCells,ANY,ANY-method setTrackingStats,trackedCells-method
The trackedCells Class.	initialize,trackedCells-method trackedCells trackedCells-class
Trajectories of 350 cells	TrajectoryDataset
Velocity AutoCorrelation	VeAutoCor
Visualize Cell Tracks originating at an Image Stack	visualizeCellTracks
Visualize Cells in an Image Stack	VisualizeStackCentroids
Data preprocessing for wound scratch assay (WSA).	wsaPreProcessing