gseacc

R

Package installation

Requirements

• Rcpp (R package)
• g++

git clone https://github.com/rocsalvador/gseacc/
cd gseacc
make install -j

Documentation

For the R documentation use ? in R. Available commands:

• ?Gsea
• ?run
• ?runChunked
• ?filterResults
• ?normalizeExprMatrix
• ?readCsv
• ?readGeneSets
• ?writeGeneSets

Example R scripts in Efficient-rank-based-statistic-for-partially-overlapping-genesets

C++

How to run

Clone and compile:

git clone https://github.com/rocsalvador/gseacc/
cd gseacc
make cc

Create a config file gsea.config in the same folder where you will run the executable:

expression-matrix-file:     relative or full path to expression matrix csv file
sep:                        csv element separator for the expression matrix csv (t for tabular)
gene-sets-file:             relative or full path to the gene sets file
sep:                        csv element separator for the gene sets file (t for tabular)
output-file:                relative or full path to the GSEA results csv
sep:                        csv element separator for the GSEA results csv (t for tabular)
threads-used:               threads used for the GSEA computation (0 to use all available threads)
normalized-data:            0 if data is not normalized, 1 if it is not
ioutput:                    number of gene sets between std output
scrna:                      0 if it is a rna experiment (runRna), 1 if it is a sc-rna experiment (runScRna)
batch-size:                 number of lines read every loop for runScRna function 

Run the executable (gsea.config must be in the same folder from where you run the executable):

./gsea

Author

Roc Salvador Andreazini (roc.salvador@estudiantat.upc.edu)