Skip to content

Commit

Permalink
Update tested MATLAB versions
Browse files Browse the repository at this point in the history
  • Loading branch information
agitter committed Jan 25, 2019
1 parent 65dbec0 commit c1fd990
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# Single-Cell Inference of Networks using Granger Ensembles (SCINGE)
Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data.
Standalone MATLAB implementation of the SCINGE algorithm. This code has been tested on MATLAB R2018a on Linux operating systems.
Standalone MATLAB implementation of the SCINGE algorithm.
This code has been tested on MATLAB R2014b and R2018a on Linux operating systems.

## Dependency
This code requires the glmnet_matlab package (http://web.stanford.edu/~hastie/glmnet_matlab/download.html).
Expand Down Expand Up @@ -29,7 +30,8 @@ Unzip `glmnet_matlab.zip` in either the root directory (that contains `SCINGE_Ex
- *influential_genes* - Genes ranked according to their SCINGE influence.

## Note on Reproducibility of Results
Because the subsampling and zero-removal stages involve pseudo-random sample removals, we generate a random seed using input hyperparameters, including the *date* input. The results can be reproduced by providing the same inputs and date from a previous experiment.
Because the subsampling and zero-removal stages involve pseudo-random sample removals, we generate a random seed using input hyperparameters, including the *date* input.
The results can be reproduced by providing the same inputs and date from a previous experiment.

## Example
`SCINGE_Example.m` demonstrates a simple example with two hyperparameter sets and two replicates.
Expand Down

0 comments on commit c1fd990

Please sign in to comment.