Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Long short-term memory recurrent neural networks for learning peptide and protein sequences to later design new, similar examples.

Simple bacterial assembly and annotation pipeline

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules

HAT is a set of tools for calling de novo variants from whole-genome sequencing data.

A bare metal Python library for building and manipulating protein molecular structures

Graphical user interface for de novo sequencing of tandem mass spectra

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.

A de novo variant caller leveraging Parabricks GPU accelerated variant calling

Tortoise is the CPU workflow of the HAT https://github.com/TNTurnerLab/HAT tools.

Transformer-based de novo sequencing (Casanovo) + database searching with rescoring (Sage + Mokapot). For metaproteomics datasets

HARE is the GPU workflow of the HAT https://github.com/TNTurnerLab/HAT tools.

Statistical models for finding de novo recurrence and compound heterozygosity across rare disease patient cohorts

A fast and accurate tool that identifies Mendelian violations in family trios. Resolve variant representation issues in VCF files