duolinwang

MusiteDeep

MusiteDeep provides a deep-learning method for general and kinase-specific phosphorylation site prediction. It is implemented by deep learning library Keras and Theano backend (the Keras2.0 and Tensorflow backend implementation were also provided under folder MusiteDeep_Keras2.0). At present, MusiteDeep only provides prediction of human phosphorylation sites; however, it also provides customized model training that enables users to train other PTM prediction models by using their own training data sets based on either CPU or GPU.

CapsNet_PTM

CapsNet for Protein Post-translational Modification site prediction.

MusiteDeep_web

This repository contains the stand-alone tool for MusiteDeep server

S-PLM

S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure

DM3Loc

A novel Deep-learning Framework with Multi-head Self-attention for Multi-label mRNA Subcellular Localization Prediction and Analyses

BFDCA

BFDCA: A Comprehensive Tool of Using Bayes Factor for Differential Co-Expression Analysis

ACM-BCB-2019-Tutorial

Slides, code, and examples for the Low-dimensional Representation of Biological Sequence Data tutorial at the ACM-BCB 2019 conference

anticrispr

August-2019-consensus-accuracy-update

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

Basecalling-comparison

A comparison of different Oxford Nanopore basecallers

Chiron

A basecaller for Oxford Nanopore Technologies' sequencers

CNNPeaks

A ChIP-Seq peak calling algorithm using convolution neural network

dragonfly

An open source python library for scalable Bayesian optimisation.

evolocity

Evolutionary velocity with protein language models

fairseq-1

Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

google-research

Google Research

gryffin

Keras-GAN-1

Keras implementations of Generative Adversarial Networks.

keras-transformer

Keras library for building (Universal) Transformers, facilitating BERT and GPT models

keras-transformer-1

Transformer implemented in Keras

memory_profiler

Monitor Memory usage of Python code

MULocDeep

MULocDeepWeb

ngl

WebGL protein viewer

ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

REDD

seq2seq-1

Minimal Seq2Seq model with Attention for Neural Machine Translation in PyTorch

taiyaki

Training models for basecalling Oxford Nanopore reads

test

vicreg

VICReg official code base