TRAPT

TRAPT is a multi-stage fused deep learning framework for transcription regulators prediction via integraing large-scale epigenomic data.

Usage

Online

We have developed a corresponding web service (https://bio.liclab.net/TRAPT). The website is designed to accepts gene sets input by users for analysis, allowing easy retrieval of analytical results. We've also thoughtfully included an email notification feature. On the results page, the website displays all TR activity scores, as well as the ranking and all individual scores of TRs. Concurrently, the website provides annotation details and relevant quality control information for each transcriptional regulator. Compared to offline tools, online analysis tools offer additional features on the browsing and result analysis pages. The online tools facilitate visualization of the predicted 3D protein structure for each TR, leveraging AlphaFold's predictions. Additionally, the online tools incorporate a genome browser to facilitate user interaction with the genomic tracks associated with each TR.

Offline

First, download library:

TRAPT library

Second, install TRAPT:

conda create --name TRAPT python=3.7
conda activate TRAPT
pip install TRAPT

Run TRAPT using a case:

Use shell commands:

# help
trapt --help
# run
trapt --library library \
      --input ESR1@DataSet_01_111_down500.txt \
      --output output/test/ESR1@DataSet_01_111_down500

Using the python interface:

import os
from TRAPT.Tools import Args, RP_Matrix
from TRAPT.Run import runTRAPT

# library path
library = 'library'
# input file path
input = 'ESR1@DataSet_01_111_down500.txt'
# output file path
output = 'output/test/ESR1@DataSet_01_111_down500'

args = Args(input, output, library)
runTRAPT(args)

De novo library

# Reconstruct TR-H3K27ac adjacency matrix
python3 src/TRAPT/DLVGAE.py H3K27ac library
# Reconstruct TR-ATAC adjacency matrix
python3 src/TRAPT/DLVGAE.py ATAC library
# Prediction D-RP(H3K27ac) matrix
python3 src/TRAPT/CalcTRSampleRPMatrix.py H3K27ac library
# Prediction D-RP(ATAC) matrix
python3 src/TRAPT/CalcTRSampleRPMatrix.py ATAC library

For more details, please visit GitHub

Please go to https://github.com/TOSTRING-Z/TRAPT