System Requirements

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CALISTA toolbox is originally written for MATLAB. The subroutines in CALISTA (version 1.2.2) have been successfully tested on MATLAB 2016b, 2017a, 2018a and 2018b.

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CALISTA-R toolbox is also provided for R users. The subroutines in CALISTA (version 1.1.2) have been successfully tested on R version 3.6.0 and RStudio Version 1.2.1335 

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Last Update

 

Current version: CALISTA-MATLAB v1.2.2 (20.02.2019) CALISTA-R v1.1.2 (16.05.2019)

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Prerequisites

 

CALISTA-MATLAB:

By default CALISTA employs Principal Component Analysis (PCA) for dimensional reduction and visualization of the expression data. Additionally, the user can also generate 2D t-SNE plots by setting INPUTS.plot_tsne = 1; in the main script as shown in this Example 7. CALISTA adopts FIt-SNE subroutines (please visit here for more details). The only prerequisite for FItt-SNE is FFTW, which can be downloaded and installed from the website.

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CALISTA-R:

CALISTA R package is built using Fortran subroutines. Before running CALISTA-R, please install the latest version of GFortran compiler.

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Download and Installation

 

CALISTA-MATLAB (MATLAB version):
Download and unzip the CALISTA-MATLAB v1.2.2.zip for codes and data.

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CALISTA-R (R version):

To install CALISTA-R directly from github repository please run the following commands in R:

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install.packages("devtools")

library("devtools")

devtools::install_github("CABSEL/CALISTA/CALISTA-R/calista")

For the old version of CALISTA-R (version 1.0.2): download and unzip the CALISTA-R v1.0.2.zip for codes and data

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License

 

Redistribution and use in source and binary forms, with or without modification, are permitted provided agreeing to the BSD 3-Clause Style License.