RT Journal Article
SR Electronic
T1 CelltrackR: an R package for fast and flexible analysis of immune cell migration data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 670505
DO 10.1101/670505
A1 Inge M. N. Wortel
A1 Katharina Dannenberg
A1 Jeffrey C. Berry
A1 Mark J. Miller
A1 Johannes Textor
YR 2019
UL http://biorxiv.org/content/early/2019/06/15/670505.abstract
AB Summary Visualization of cell migration via time-lapse microscopy has greatly advanced our understanding of the immune system. However, subtle differences in migration dynamics are easily obscured by biases and imaging artifacts. While several analysis methods have been suggested to address these issues, an integrated tool implementing them is currently lacking. Here, we present CelltrackR, an R package containing a diverse set of state-of-the-art analysis methods for (immune) cell tracks. CelltrackR supports the complete pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Availability and Implementation CelltrackR is an open-source package released under the GPL-2 license, and is freely available on GitHub at https://github.com/ingewortel/celltrackR.Contact mmiller23{at}wustl.edu, Johannes.Textor{at}radboudumc.nl