denovo

There are 27 repositories under denovo topic.

  • topazape/LSTM_Chem

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

    Language:Jupyter Notebook11691656

  • sirius-ms/sirius

    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)

    Language:Java901021923

  • alexarnimueller/LSTM_peptides

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

    Language:Python715626

  • nf-core/bacass

    Simple bacterial assembly and annotation pipeline

    Language:Nextflow631516742

  • Shamir-Lab/Recycler

    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

    Language:Python579317

  • sirius-ms/sirius-libs

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

    Language:Java517025

  • sarisabban/RamaNet

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

    Language:Python493110

  • topazape/molecular-VAE

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

    Language:Python443219
  • HAT

    TNTurnerLab/HAT

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

    Language:Python23210

  • sarisabban/Pose

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

    Language:Python16303

  • compomics/denovogui

    Graphical user interface for de novo sequencing of tandem mass spectra

    Language:Java1414477

  • bgm-cwg/novoCaller

    Language:C++8531

  • nf-core/denovohybrid

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

    Language:Nextflow8235
  • acorn

    TNTurnerLab/acorn

    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.

    Language:R6210

  • TNTurnerLab/Hare

    A de novo variant caller leveraging Parabricks GPU accelerated variant calling

    Language:Python6200

  • TNTurnerLab/Tortoise

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

    Language:Python5220

  • yc386/orthrus_metaproteomics

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

    Language:Jupyter Notebook52

  • TNTurnerLab/GPU_accelerated_de_novo_workflow

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

    Language:Shell4300

  • hms-dbmi/RaMeDiES

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

    Language:Python3300

  • BerkeCagkanToptas/VBT-TrioAnalysis

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

    Language:C++2010

  • maybelinot/findltr

    De novo identification of LTR retrotransposons

    Language:Python2431

  • aradar46/denovo-assembly-long-read

    Part of BINP29 course

    Language:HTML1210

  • Nkts007/Research-Project

    This repository holds the code and notes during the use of Casanovo as part of my Research Project, as well as links to resources used as part of the Metaproteomic Analysis of my samples.

    Language:Jupyter Notebook1100

  • 0-Ioniel-0/guppy_MR

    Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.

    Language:Python0101

  • ai4u-ai/ai4chem

    Deep Learning for Chem

    Language:Python0101

  • parthian-sterlet/mcot-kernel

    Detection of motifs co-occurrence in a single ChIP-seq dataset

    Language:C++0000

  • thilus/ms-tagger

    Graph-based algorithm for generating peptide tags from MS/MS data

    Language:Java0100