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deep_learning_examples

Examples of using deep learning in Bioinformatics

deeplearning-biology

A list of deep learning implementations in biology

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

deeprank-gnn-esm

Graph Network for protein-protein interface including language model features

demo

dl2bioinformatics

Deep learning with bioinformatics

dnngp

DNNGP: Deep neural network for genomic prediction

dupgen_finder

A pipeline used to identify different modes of duplicated gene pairs

easycodeml

easyspeciestree

Easily construct the ML species tree with single-copy gene shared by different species.

effectr

An R package to call oomycete effectors

efficient-evolution

Efficient evolution from protein language models

eigenfold

EigenFold: Generative Protein Structure Prediction with Diffusion Models

equibind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

equidock_public

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

eternafold

Improving RNA structure prediction through multitask learning on diverse crowdsourced data.

evolution

This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'

export

R package for streamlined export of graphs and data tables.

external-attention-pytorch

🍀 Pytorch implementation of various Attention Mechanisms, MLP, Re-parameter, Convolution, which is helpful to further understand papers.⭐⭐⭐

exutr

ExUTR is a practical and powerful tool that enables rapid genome-wide 3'-UTR prediction from massive RNA-Seq data

finder

A fully automated gene annotator from RNA-Seq expression data

free-python-games

Free Python Games

funannotate

Eukaryotic Genome Annotation Pipeline

fungap

FunGAP: fungal Genome Annotation Pipeline

genome_analysis

For genome assembly, annotation, and comparative genomics.

genome_annotation

These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to follw

genomeworks

SDK for GPU accelerated genome assembly and analysis

geta

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science