Code and data for Larocque et al. manuscript #p054p031
Intracellular nanovesicles mediate α5β1 integrin trafficking during cell migration
Gabrielle Larocque, Daniel J. Moore, Méghane Sittewelle, Cansu Kuey, Joseph H.R. Hetmanski, Penelope J. La-Borde, Beverley J. Wilson, Nicholas I. Clarke, Patrick T. Caswell and Stephen J. Royle
J Cell Biol, 220: e202009028 doi: 10.1083/jcb.202009028
cell_migration
cell track data in excel workbooks or directories of CSV files for analysis using CellMigrationcell_shape
IMOD models and corresponding text files (produced bymodel2point
) for analysis using CellShapevariance
excel workbooks with spatiotemporal data for Rab GTPases and TPD54 mutants.
Data for R plots are in the R
directory.
ImageVariance.ipf
a workflow to analyze cropped images for spatiotemporal variance in IgorProMakeEffectSizeGraph.ipf
simple graphing procedure using R output of estimation statistics e.g.rabscreen_figure
MitoAggregation.ipf
analysis of outputs from the Fiji scriptMitoAggregation.ijm
which will extract statistics of mitochondria from cell limagesProteomicsProcs.ipf
a workflow used in conjunction with VolcanoPlot
Three R projects to generate plots in the paper.
cancer_figure
- plotting data from TCGAheatmap_figure
- hierarchical clustering of Rab screen datarabscreen_figure
- calculating effect sizes from raw data
All work in a similar way. Data files are in the Data
directory and are processed by an R script in Script
to generate outputs that are saved to Output/Data
or Output/Plots
.