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c_amps-prediction

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deept2

DeepT2 utilizes deep learning techniques to identify type II polyketide (T2PK) synthases KSβ and their corresponding T2PK product within bacterial genomes. The method leverages ESM2 to transform KSβ sequences into embeddings, which are employed to train two separate classifiers using multi-layer perceptron for both KSβ and T2PKs classification.

denovogenomeassembly

A pipeline for De Novo Genome Assembly

diffdock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

difflinker

DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design

drep

Rapid comparison and dereplication of genomes

dynamicbind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

efficient-evolution

Efficient evolution from protein language models

endophytegenomes

Scripts for Hill et al. (2023) doi:10.1093/gbe/evad038 🌿

equibind

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

esm

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

esp3d-webui

A Web UI for ESP8266 or ESP32 based boards connected to 3D printers / CNC

eukheist

eukmetasanity

Structural and functional annotation of eukaryotic metagenome-assembled genomes

eukrep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

euksemble

Pipeline for identification of eukaryotic contigs in metagenomic assemblies

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

evoplay

fine

funannotate

Eukaryotic Genome Annotation Pipeline

fungiflow

Reproducible Python workflow for identifying biosynthetic gene clusters from fungal sequence data.

funomic

funorder

The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution – novel tool that allows automated identification of essential genes in a biosynthetic gene clusters (BGC) based solely on genomic data

fusariumlifestyles

Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085

gappredict

Character-level language model for draft genome assembly gap-filling

genome-assembly-pipeline

De novo genome assembly pipeline to assemble short, paired end, illumina genome sequences of unknown microbes

genome_assembly_pipeline

General purpose assembly and annotation pipeline

getting-things-done-with-pytorch

Jupyter Notebook tutorials on solving real-world problems with Machine Learning & Deep Learning using PyTorch. Topics: Face detection with Detectron 2, Time Series anomaly detection with LSTM Autoencoders, Object Detection with YOLO v5, Build your first Neural Network, Time Series forecasting for Coronavirus daily cases, Sentiment Analysis with BER

gpt-engineer

Specify what you want it to build, the AI asks for clarification, and then builds it.