DeepdlncUD

tags: lncRNA drugs gene regulation

Overview

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This repository is a standalone package of the DeepdlncUD method. DeepdlncUD is used to predict the regulation types of small molecules on modulating lncRNA expression. This method is powered by 9 deep learning models.

Installation

• PyPI

pip install deepdlncud

Overview

deepdlncud [-h]
           --method m
           --smile_fpn sm
           --fasta_fpn lncr
           --model_fp mf
           --output_path o

argument details:
    -h, --help            show this help message and exit
    -m, --method,
            A deep learning method. It can be any below.
            DenseNet18 | CNN | ConvMixer64 | DSConv | LSTMCNN | MobileNet | ResNet18 | ResNet50 | SEResNet


    -sm, --smile_fpn, a small molecule file that contains only smile strings


    -lncr, --fasta_fpn, a lncRNA fasta file


    -mf, --model_fp, a model path


    -o, --output_path, outputting deepdlncud predictions

Usage

Download models

see models https://github.com/2003100127/deepdlncud/releases/tag/model

deepdlncud_download # this is to download the model in your current folder

# output messages
downloading...
downloaded!

Please use -mf of deepdlncud then to access to where the models are located.

Input format

Two example files in DeepdlncUD are 60606.txt and HIF1A-AS1.fasta for a small molecule and a lncRNA molecule.

• Clopidogrel (small molecule CID: 60606)

# 60606.txt
COC(=O)[C@H](C1=CC=CC=C1Cl)N2CCC3=C(C2)C=CS3

• hsa-let-7e-5p (lncRNA)

# HIF1A-AS1.fasta
>HIF1A-AS1
CGCCGCCGGCGCCCTCCATGGTGAATCGGTCCCCGCGATGTCTTCACGGCGGGCGGCCCCCAGGCTCGCTCCGGCCTAAGCGCTGGCTCCCTCCACACGCGGAGAAGAGAAGGAAAGACTACAGTTCAACTGTCAATTGGTTGATCACCCGGATTTTATCTACACCTTAGCCTATGGTTGTTCATCTCGTCTCTGCCTATGGCCCATTGACTCCCGGATCCCAGCTCCATTCTTCGGTACTTTACGCACCCTGCTTCCAGTACCCCAACCAGAAGAATATATATAGCAGTTAACTGTCAGCTGGCGAAAAGGAGGAAAATTCAGGAAGATAAAATAGCTGAATGAATTATCCCCGCTCCAGAACGCAGAGGAAAAATGAAATGGCCAGACCCAGATGTTAAAAATGTGTTCCTTGCTCTTTCCTGCCCTAGCAAGGGCTGTTCCATGTTTAGGGGATGAATGCCGCTGAGAGTATTAGCAAAAATACATGTGTCATTGAGTCTGAGGAAGATAACTGAGACATACAGGTATTTCTCATAATGCATGTGGGCATCCATAGACATATTCTTAAATGGCTTAAGGACTTGGAAACTACCTCTAGGAAACCTGAAACTTGAATGTTGGTCCACTAGGGAGAAGAAATGTTCCATTA

Inference

Use two example files in DeepdlncUD. The ConvMixer64 model is recommanded to use in your studies.

deepdlncud -m LSTMCNN -sm deepdlncud/data/example/60606.txt -lncr deepdlncud/data/example/HIF1A-AS1.fasta -mf /the/path/you/prefer/model/lstmcnn -o ./out.deepdlncud

Citation

Please cite our work if you use DeepdlncUD in your research.

Contact

If you have any question, please contact Jianfeng Sun. We highly recommend creating issue pages when you have problems. Your issues will be responded then.