TRAP - Time-series RNA-seq Analysis Package

Installing TRAP in two ways

1. git clone https://github.com/kyuriJo/TRAP.git

2. Download the file to your linux server.
Unzip by 'tar -xvf TRAP_2.3.tar.gz' or 'unzip TRAP_2.3.zip'.

Download TRAP 2.3 (tar.gz) (Updated on 2015-08-07)

Download TRAP 2.3 (zip) (Updated on 2015-08-07)

Prerequisite for TRAP

TRAP needs Python and following Python packages.
Click to download and install each package.

- SciPy

- NumPy

- NetworkX (ver. 1.5 ~)

- matplotlib

Running TRAP

- Fill in 'TRAP/config.txt' as described in the README file.

- If you already have Tophat, Cufflinks or Cuffdiff result, put it in 'TRAP/tophat_result/SAMPLE/' or 'TRAP/cufflinks_result/SAMPLE/' or 'TRAP/cuffdiff_result/SAMPLE/' for each sample.
(You can start with Cufflinks or Cuffdiff results only.)

- Run TRAP by typing './TRAP'.

TRAP Updates

- 2015/08/07 : TRAP 2.3	Added a function to print out nodes and edges of the pathway network.
- 2015/06/08 : TRAP 2.2	Fixed a bug of not showing node names in the graph image.
- 2015/05/27 : TRAP 2.1	Fixed errors and updated to use Cuffdiff p-value for clustering
- 2014/08/28 : TRAP-web	Updated by adopting the features of TRAP 2.0.
- 2014/07/18 : TRAP 2.0	An improvement on calculating pPERT and pathway status.
- 2014/05/21 : TRAP 1.71	Fixed a bug due to the difference of KEGG gene ID format among organisms.
- 2014/04/14 : TRAP 1.7	Fixed a bug of miscalculation of pPERT in pathway analysis.
- 2014/04/06 : TRAP 1.6	Fixed a bug in Clustering.py.
- 2014/03/26 : TRAP 1.5	Fixed to support multiple replicates. Fixed to deal with a bug from Scipy module.
- 2014/02/26 : TRAP 1.1	Fixed to identify group entry in kgml files. Fixed to differentiate genes with same gene name but in different entries. With more readable alignment of text in output files.
- 2014/02/15 : TRAP 1.0	Added license into the source code. Fixed a bug that reading wrong columns from Cufflinks result.
- 2014/02/05 : TRAP 1.0	.

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