adalisan

deeplearning-models

A collection of various deep learning architectures, models, and tips

deeplexicon

Signal based nanopore RNA demultiplexing with convolutional neural networks

dotfiles

Protein3D

pySAR_proteinseq_aa

Analysing Sequence Activity Relationships (SARs) of protein sequences and their mutants using Machine Learning.

ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers

a Transformer-based neural network for generating highly optimized protein sequences called Regularized Latent Space Optimization (RELSO)

awesome-awesomeness

A curated list of awesome awesomeness

aaindex

Python package for AAIndex database (https://www.genome.jp/aaindex/)

ASHURE

Python-based pipeline for analyzing Nanopore sequencing metabarcoding data

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

biotools

A list of useful bioinformatics resources

configurations-linux

My Linux Machine Configurations

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dgl-lifesci

Python package for graph neural networks in chemistry and biology

dms_tools2

software for the analysis and visualization of deep mutational scanning data

Enrich2

Tool for deep mutational scanning experiments.

EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

EVE_fork

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

Genomic-ULMFiT

ULMFiT for Genomic Sequence Data

IsoSeq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

mutect2

Workflow to run Mutect2 (GATK4)

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

RMSF-net

rRNA_nanoSHAPE

Code accompanying "Direct detection of RNA modifications and structure using single molecule nanopore sequencing"

scientific-python-cookiecutter

a tutorial and 'cookiecutter' template for a scientific Python library

SEMAi

Spatial Epitope Modeling with Artificial intelligence (SEMA)

smrtsv2

Structural variant caller for PacBio

strelka

Strelka2 germline and somatic small variant caller

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing