Skip to content

@Shamir-Lab Ron Shamir's Lab

Change the repository type filter

All

    Repositories list

    36 repositories

    • 4CAC

      Public
      Python
      •
      MIT License
      •1•2•1•1•Updated Aug 28, 2024Aug 28, 2024

    • PlasClass

      Public
      A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007781
      Python
      •
      MIT License
      •7•26•2•1•Updated Jun 17, 2024Jun 17, 2024

    • syncmer_mapping

      Public
      Implementations of syncmer-based long read mappers
      C
      •
      MIT License
      •1•6•0•0•Updated Mar 8, 2024Mar 8, 2024

    • ABXAppropriatenessML

      Public
      Prediction of ABX appropriateness in ICU inpatients
      Python
      •0•0•0•0•Updated Mar 3, 2024Mar 3, 2024

    • PRS-imputation-panels

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • DOMINO

      Public
      Network-based module discovery algorithm with high rate of empirically-validated term calls
      Python
      •
      MIT License
      •2•9•3•0•Updated Oct 22, 2023Oct 22, 2023

    • StatTheGit4TAU

      Public
      Maintain GitHub Stats for More than 14 Days
      Python
      •
      MIT License
      •4•0•0•0•Updated Aug 29, 2023Aug 29, 2023

    • EnhancerSilencerDL

      Public
      Codebase for inferring single nucleotide activation and repression maps using deep-learning
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • FRIGATE

      Public
      Frigate - Feature ranking for clustering using game theory
      Python
      •0•0•0•0•Updated Aug 8, 2023Aug 8, 2023

    • domino_web

      Public
      HTML
      •2•1•0•1•Updated Jul 7, 2023Jul 7, 2023

    • clustering_echo_covid

      Public
      using k-prototype algorithm on mixed-type medical data
      Python
      •0•1•0•0•Updated Mar 14, 2023Mar 14, 2023

    • SCAPP

      Public
      SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z
      Python
      •
      MIT License
      •6•29•7•0•Updated Feb 26, 2023Feb 26, 2023

    • INTEND

      Public
      INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples
      machine-learning-algorithmsmulti-omicsmulti-omic-integration
      R
      •0•8•1•0•Updated Dec 12, 2022Dec 12, 2022

    • 3CAC

      Public
      Java
      •
      MIT License
      •0•2•0•0•Updated Apr 6, 2022Apr 6, 2022

    • PRODIGY

      Public
      Personalized prioritization of driver genes in cancer
      R
      •3•9•0•0•Updated Mar 14, 2022Mar 14, 2022

    • AdaOrder

      Public
      Java
      •
      MIT License
      •0•1•0•1•Updated Jan 13, 2022Jan 13, 2022

    • covid19-mnews

      Public
      Python
      •0•0•0•0•Updated Dec 20, 2021Dec 20, 2021

    • DGerbil

      Public
      A fast and memory-efficient k-mer counter with GPU-support
      C++
      •
      MIT License
      •14•0•0•1•Updated Aug 4, 2021Aug 4, 2021

    • EMP

      Public
      EMpirical Pipeline for correcting GO terms obtained by network-based module discovery algorithms.
      Python
      •0•1•0•0•Updated Jun 3, 2021Jun 3, 2021

    • EMP-benchmark

      Public
      EMP-based benchmark for Network-based discovery of activity modules
      Python
      •0•0•0•0•Updated Jun 3, 2021Jun 3, 2021

    • Recycler

      Public
      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
      assemblydenovorecyclerassembly-graphplasmidmetagenomescircular-sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•58•9•0•Updated Apr 22, 2021Apr 22, 2021

    • MSP_UHS

      Public
      Java
      •0•1•0•0•Updated Nov 14, 2020Nov 14, 2020

    • Logrank-Inaccuracies

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 9, 2020Sep 9, 2020

    • Multi-Omics-Cancer-Benchmark

      Public
      R
      •
      GNU General Public License v3.0
      •17•25•2•1•Updated Sep 8, 2020Sep 8, 2020

    • MONET

      Public
      MONET
      graph-algorithmsclusteringmulti-omics
      R
      •0•6•0•0•Updated Sep 4, 2020Sep 4, 2020

    • NEMO

      Public
      R
      •
      GNU General Public License v3.0
      •3•15•1•0•Updated May 5, 2020May 5, 2020

    • CT-FOCS

      Public
      Codebase for CT-FOCS, a new method for inferring cell type-specific enhancer-promoter (EP) links and for integrative analysis of EP links
      R
      •1•4•0•0•Updated Jul 18, 2019Jul 18, 2019

    • DOCKS

      Public
      Java code for DOCKS algorithm
      Java
      •1•3•0•1•Updated Jan 4, 2019Jan 4, 2019

    • Karyotype-reconstruction

      Public
      An ILP based algorithm to reconstruct karyotypes, and a karyotype simulator. The algorithm is described in the manuscript bioRxiv 152447; doi: https://doi.org/10.1101/152447
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Aug 20, 2018Aug 20, 2018

    • SPRINT

      Public
      This R code reproduces the results presented in: "Personalized prediction of adverse heart and kidney events using pre-enrollment and time course data from SPRINT and ACCORD trials"
      R
      •0•0•0•0•Updated Aug 20, 2018Aug 20, 2018