Protein Fold Change

Protein Fold Change filters a protein table according to the peptides fold change (FC) of the proteins. If at least x % of the peptides are above or below a target FC, then the protein is selected. By default Protein Fold Change selects all the proteins with at least 80% of their peptides with a FC > 2 or FC <0.5.

Manual :

1- install Julia free programming language and install package :

DataFrames : Pkg.add("DataFrames")

2- unzip the software

3- edit config file in the config directory and enter the names of :

# column name of proteins

protRow=PG_ProteinNames

# column name of peptides

pepRow=EG_PrecursorId

# column name of fold change

FCRow=FC

4- copy your n tables in csv (TAB delimitated by default) files in the “data” directory.

- first line of the table : column names with at least 3 columns : protein names, peptide names and FC

- next lines : values

5- execute the software by the command : julia software_name

6- results tables are in the results directory.