README.md

stExpressionViewer

This software is currently under development.

R software for visualizing the gene expression in the atlas from ST data. 16GB of RAM or more is strongly recommended. Data is not public yet but will be after publication.

How to install

1/ Install R (https://cran.r-project.org/bin/macosx/, link R-3.5.1.pkg or R-3.3.3.pkg depending on your mac version). Then run R.

2/ Enter in R console the command:\ install.packages("devtools", dependencies = TRUE)\ If asked: "Do you want to install from sources the packages which need compilation?" say "n" (no) \ If asked for mirror, pick any of them (preferably geographically close)

3/ R command:\ library(devtools)

4/ R command:\ install_github("cantin-ortiz/stExpressionViewer")

How to use

1/ R command: (load the library)\ library(stExpressionViewer)

2/ R command: (replace this path by the one to the data folder that is provided separately)\ path <- 'C:/Users/MatLab/Desktop/st-project/data'

3/ R command (start the software)\ st.expression.viewer(path)

4/ If you are Windows user, you should specify it with the boolean os.windows:\ st.expression.viewer(path, os.windows = TRUE)

5/ You can change the size of the visualization window with the parameter win.dim. The default value is 14x14. Use higher values for increasing the size, lower values for making the window smaller. For instance:\ st.expression.viewer(path, win.dim = c(10,10))

For a Windows user, combine both parameters:\ st.expression.viewer(path, win.dim = c(10,10), os.windows = TRUE)



cantin-ortiz/stExpressionViewer documentation built on Oct. 10, 2018, 3:18 p.m.