Spindle analysis tool is an open-source cluster of tools with its ongoing development for meiotic and mitotic spindle analysis. Key futures:
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Online access
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Simple and intuitive to use with implemented UI. Only require installation of the R software environment and optional Rstudio.
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It is designed from the ground up to incrementally scale up this tool based on evolving use cases.
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Allows working on projects reproducibly and compare data.
Spindle analysis tool aims to replace huge and complicated to work with a spreadsheet that is frequently used for Spatial Graph analysis, but also it allows to uniform and completely automate analysis.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. You can run the software in an online-version under the Shinyapp.io or localy.
* Clean spatial graph and manual check all microtubules for its correct segmentation
* Create a point for a center of centrioles and label them Pole1 and Pole2
* Reorient spatial graph in a way that Pole1 correspond to the bottom of a spindle and Pole 2 to the top
* Rotate spatial graph to align labels Pole1 and Pole2 their position in X and Y
* Label selected classes of MT. For example: Pole1_00, Pole1_01, etc.
* Using Amira calculate MT length
R v3.5.3 or newer
Rstudio v1.2 or newer
Java SE 11 (LTS)
R library
- shiny
- shinycssloaders
- shinyWidgets
- shinyBS
- shinyalert
- colourpicker
- readxl
- plyr
- tidyverse
- ggplot2
- egg
- base
- alphashape3d
- xlsx
- zip
install.packages("remotes")
remotes::install_github("RRobert92/ASGA")
library(shiny)
runApp("ASGA")
For portable ASGA application:
git clone https://github.com/RRobert92/ASGA
cd ASGA
run Distribution_Creat.ps1
Contributions, collaborators and/or constructive criticism are welcome! Please see our Contributing Guide "Soon available" for more details.
This project is distributed under the General Public License (GPL) version 3.0 - see the LICENSE.md file for details.
Kiewisz R. Spindle analysis tool (2020) DOI: 10.5281/zenodo.3732108