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@rajewsky-lab Systems Biology of Gene Regulatory Elements (N. Rajewsky lab)

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    30 repositories

    • spacemake

      Public
      Python
      •
      Other
      •13•49•8•4•Updated Apr 21, 2026Apr 21, 2026

    • rajewsky-lab.github.io

      Public
      Lab website
      HTML
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • mirdeep2

      Public
      Discovering known and novel miRNAs from small RNA sequencing data
      analysismappingsequencing
      analysismappingsequencingpredictionquantificationmirnasmallrnamicrorna
      Perl
      •
      GNU General Public License v3.0
      •54•159•3•1•Updated Dec 11, 2025Dec 11, 2025

    • openst

      Public
      Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
      bioinformaticsomicstranscriptomics
      bioinformaticsomicstranscriptomicsspatial-transcriptomics
      HTML
      •
      Other
      •21•112•18•3•Updated Jul 4, 2025Jul 4, 2025

    • 3D_lung

      Public
      Code avaliability for the publication 'Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions the tumor microenvironment'
      Python
      •0•7•0•0•Updated Apr 11, 2025Apr 11, 2025

    • stimwrap

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•7•1•0•Updated Feb 26, 2025Feb 26, 2025

    • Huntington_midbrain_organoids

      Public
      Code related to single cell transcriptomic analyses in the manuscript 'Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediat…
      0•1•0•0•Updated Jun 26, 2024Jun 26, 2024

    • .github

      Public
      1•0•0•1•Updated Jun 26, 2024Jun 26, 2024

    • HSV1_cerebral_organoids

      Public
      Code related to the manuscript 'Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids'
      0•0•0•0•Updated Apr 11, 2024Apr 11, 2024

    • novosparc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •42•132•8•3•Updated Nov 17, 2023Nov 17, 2023

    • Eskrate

      Public
      R
      •1•3•1•1•Updated Aug 30, 2023Aug 30, 2023

    • optocoder

      Public
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Nov 29, 2022Nov 29, 2022

    • octopus_microRNAs

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Nov 13, 2022Nov 13, 2022

    • novosparc_workshop

      Public
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Jun 1, 2022Jun 1, 2022

    • optocoder_scripts

      Public
      Python
      •0•1•0•0•Updated Apr 29, 2022Apr 29, 2022

    • spacemake-test-data

      Public
      Collection of optional sequencing read data for spacemake testing.
      MIT License
      •0•0•0•0•Updated Mar 24, 2022Mar 24, 2022

    • FLAMAnalysis

      Public
      Data Analysis For FLAM-Seq Third Generation RNA Sequencing
      Python
      •3•9•3•1•Updated Jan 22, 2022Jan 22, 2022

    • SLAM-Drop-seq

      Public
      Python
      •1•1•0•0•Updated Jan 20, 2022Jan 20, 2022

    • distmap

      Public
      DistMap
      R
      •
      MIT License
      •9•13•0•0•Updated Nov 23, 2021Nov 23, 2021

    • SPACEGERM

      Public archive
      SPACEGERM shiny app (archived, see GitLab for active fork)
      shiny-appsspatial-clusteringgene-expression-profiles
      shiny-appsspatial-clusteringgene-expression-profilesvirtual-in-situ-hybridization
      R
      •
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Nov 9, 2018Nov 9, 2018

    • helpers

      Public
      'useful' little helper scripts for the day-to-day life in the N. Rajewsky dry lab
      Perl
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Sep 28, 2018Sep 28, 2018

    • planarian_lineages

      Public
      Jupyter Notebook
      •7•27•3•0•Updated Apr 18, 2018Apr 18, 2018

    • dropbead

      Public
      HTML
      •8•6•6•0•Updated Feb 21, 2018Feb 21, 2018

    • byo

      Public
      python library for efficient low-level stuff to access all kinds of data and cool high level things like transcripts, splicing, etc.
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 27, 2016Nov 27, 2016

    • PyMAF

      Public
      Easy handling of MAF files and many genomes
      Python
      •
      GNU General Public License v3.0
      •1•1•1•0•Updated Nov 27, 2016Nov 27, 2016

    • polyA

      Public
      Python
      •1•0•14•0•Updated Sep 12, 2016Sep 12, 2016

    • bioanalyzer-profile

      Public
      Analyze raw data from bioanalyzer
      R
      •0•2•0•0•Updated Sep 12, 2016Sep 12, 2016

    • find_circ2

      Public
      Find circRNAs in RNA-seq data.
      Python
      •
      GNU General Public License v3.0
      •7•15•1•0•Updated Jul 5, 2016Jul 5, 2016

    • find_circ

      Public
      Find circRNAs in RNA-seq data.
      Python
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Mar 3, 2016Mar 3, 2016

    • clip_analysis

      Public
      Scripts to analyze (PAR-)CLIP data.
      Python
      •
      GNU General Public License v3.0
      •5•2•0•0•Updated Mar 9, 2015Mar 9, 2015
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