tanlabcode/pangea repository overview

PANGEA: Predictive Analysis of Noncoding Genomic Enhancer/Promoter Alterations

I. Preparation of the input files

1. Gene expression in patients. Format: [Patient ID]\t[FPKM]\n

2. EP pairs. Format: [Enh-Chr]\t[Enh-Start]\t[Enh-End]\t[Pro-Chr]\t[Pro-Position]\t[Gene]\n

3. Patient IDs. Format: [ID]\n

4. SNVs in patients. Format: [Patient ID]\t[Chr]\t[Position]\n

5. Translocation/Inversion break points. Format: [Patient ID]\t[BP1-Chr]\t[Position]\t[Strand]\t[BP2-Chr]\t[Position]\t[Strand]\n

6. Duplication/Deletion break points. Format: [Patient ID]\t[BP1-Chr]\t[Position]\t[Strand]\t[BP2-Chr]\t[Position]\t[Strand]\n

II. Usage:

docker run -v "$PWD":/app tanlabcode/pangea:latest perl /home/PANGEA.pl 
       -n [gene name] 
       -g [gene expression] 
       -p [list of patients]
       -e [EP pairs]
       -a [SNV]
       -b [TRAN/INV]
       -c [CNV]

III. Example:

A set of example input files are built into the package. Use following command to run PANGEA with the example:

docker run -v "$PWD":/app tanlabcode/im-pet:latest perl /home/PANGEA.pl 
       -n CBFB
       -g /home/Example_Input/CBFB_AML.txt
       -p /home/Example_Input/AML_patients.txt
       -e /home/Example_Input/AML_EP_chr16.txt
       -a /home/Example_Input/AML_chr16_snv.txt
       -b /home/Example_Input/AML_chr16_bp.txt
       -c /home/Example_Input/AML_chr16_cnv.txt