Package: cellmigRation 1.21.0

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]

cellmigRation_1.21.0.tar.gz
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cellmigRation_1.21.0.tgz(r-4.6-any)cellmigRation_1.21.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cellmigRation/json (API)

# 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-1.21.0(bioc 3.24)cellmigRation-1.20.0(bioc 3.23)

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

4.60 score 1 stars 4 scripts 67 exports 147 dependencies

Last updated from:ed6d00a32e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	221
linux-devel-x86_64	NOTE	295
source / vignettes	OK	340
linux-release-x86_64	NOTE	357
macos-release-arm64	NOTE	131
macos-oldrel-arm64	NOTE	116
windows-devel	NOTE	197
windows-release	NOTE	287
windows-oldrel	NOTE	326
wasm-release	OK	183

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 commonmark cowplot cpp11 crosstalk curl data.table Deriv deSolve digest doBy doParallel dplyr DT ellipse emmeans estimability evaluate FactoMineR farver fastmap flashClust FME fontawesome foreach forecast foreign Formula fracdiff fs generics ggplot2 ggrepel ggtext glue gridExtra gridtext gtable highr Hmisc htmlTable htmltools htmlwidgets irlba isoband iterators jpeg jquerylib jsonlite knitr labeling later lattice lazyeval leaps lifecycle litedown lme4 lmtest magic magrittr markdown MASS Matrix MatrixModels matrixStats memoise mgcv mime minpack.lm minqa modelr multcompView mvtnorm nlme nloptr nnet numDeriv otel pbkrtest pillar pkgconfig plyr png promises purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rmarkdown rootSolve rpart rstudioapi S7 sass scales scatterplot3d showtext showtextdb sm sp SparseM SpatialTools spBayes stringi stringr survival sysfonts tibble tidyr tidyselect tiff timeDate tinytex urca utf8 vctrs vioplot viridisLite withr xfun xml2 yaml zoo

cellmigRation

Rendered fromcellmigRation.Rmdusingknitr::rmarkdown

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