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2drna-fold

Learning RNA Folding Path based on Reinforcement Learning and Monte Carlo Tree Search

arnie

Python utility to estimate, compare, and reweight RNA energetics across many secondary structure algorithms.

assemblies-of-putative-sars-cov2-spike-encoding-mrna-sequences-for-vaccines-bnt-162b2-and-mrna-1273

RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences a

awesome-mlops

:sunglasses: A curated list of awesome MLOps tools

bioautomated

Automated machine learning for analyzing, interpreting, and designing biological sequences

bprna

bpRNA: Large-scale Annotation and Analysis of RNA Secondary Structure

captum

Model interpretability and understanding for PyTorch

cdsfold

circshapemapper

codecommit-sync-action

cookiecutter-pytorch-lightning

Cookiecutter PyTorch Lightning

cookiecutter-r-analysis

Cookiecutter template for an R analysis project

deep-learning-project-template

Pytorch Lightning code guideline for conferences

deepcip

A deep learning method for the prediction of internal ribosome entry sites (IRES) of circRNAs

deepdru

Decipher the rules which mRNA structure differs in vivo and in vitro by deep neural networks

detect-mutations

Python script for detecting mutations in aligned reads (.bam |.sam) e.g. from RNA base conversion techniques such as TimeLapse, SLAM-seq, TUC-seq

dl-rna

dnachisel

:pencil2: A versatile DNA sequence optimizer

eternafold

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

fastqsplitter

Splits fastq files evenly

gsae

Code from 'Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph Embeddings"

icor-codon-optimization

RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8

llama

Inference code for LLaMA models

markovgnn

PyTorch-Geometric Implementation of MarkovGNN method published in Graph Learning@WWW 2022 titled "MarkovGNN: Graph Neural Networks on Markov Diffusion"

mxfold2

MXfold2: RNA secondary structure prediction using deep learning with thermodynamic integration

paper-5utr-design

Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"

pytorch-lightning-cookiecutter

Cookiecutter template for PyTorch Lightning Projects

pytorch-template

PyTorch deep learning projects made easy.

r-package-template

A template for R packages

r2dt

Visualise RNA secondary structure in consistent, reproducible and recognisable layouts