t-SNE

This software computes the t-SNE distribution map of an unlimited number of files. Computations are based on the t-SNE R package and parallelization is done with GNU parallel.

Manual :

1- if not already installed, install Perl free programming language

2- install R programming language and t-SNE.

install.packages("tsne")

3- install GNU parallel (GNU Linux only)

4- unzip the software

5- copy data tsv files (TAB separator) in the “data” directory :

- first line : columns names

- first column : categories

example :

categorie ABCB1

NK 7.6 7.6

NK 7.6 7.7

T_CD4 5.6

T_CD4 5.15

next columns are the values, with separator TAB.

6 - edit conf.txt to set the number of parameters

7- edit t-SNE-003.r to set your t-SNE parameters

8- execute the software by the command : perl parallel_tsne-0.1.pl

9- plots are in the "svg" directory