FUNAGE-Pro

Functional analysis of Prokaryotes using Gene Set Enrichment Analysis on Transcriptome (RNA-Seq) or Proteome data

update 2022-Apr-19, Name change from GSEA-Pro to FUNAGE-Pro

INSTALL FUNAGE-Pro

1. Clone FUNAGE-Pro from github
2. Install R 3.4 or newer, if not available
3. Install Perl 5.26 or newer, if not available
4. Install Python 3.6 or newer, if not available
5. goto the gsea_pro folder and run

./gsea_pro_v3.pl

• -s sessiondir and output folder [default=current folder]
• -table Tab delimited text file of locus-tags and experiments: first column = locus_tag, other columns = experiments
• -g genome prefix, including full path [e.g. /var/genomes/Bacteria/Lactococcus_lactis_cremoris_MG1363_uid58837/NC_009004 ]
• -method analyzing method: experiment | cluster [ default = experiment ]
• -up cutoff value for positive values [default = 2]
• -down cutoff value for negative values [default = -2]
• -cluster Name of the clustercolumn [default = clusterID]
• -auto Auto detect threshold values [default= true]
• -o user prefix for results [default = gsea_pro ]

4. Example command line: ./gsea_pro_v3.pl -table gsea_pro_Experiment_Table.txt -g /var/genomes/Bacteria/Bacillus_subtilis_168_uid57675/NC_000964 -o my_results

INSTALL FACoP locally

1. goto the FACoP subfolder of FUNAGE_Pro
2. run the script 00.FUNAGEpro_build_database.sh
3. run the script 01.GSEApro_annotate_genomes.sh
4. Install DIAMOND on your server; Benjamin Buchfink, Chao Xie & Daniel H. Huson, Fast and Sensitive Protein Alignment using DIAMOND, Nature Methods, 12, 59–60 (2015) doi:10.1038/nmeth.3176.)