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    26 repositories

    • genomepy

      Public
      genes and genomes at your fingertips
      pythongenomeensemblbiocondaucscncbi
      Python
      •
      MIT License
      •38•383•17•1•Updated Dec 18, 2024Dec 18, 2024

    • GBD_data

      Public
      Datasets for the Genomics and Big Data course
      0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • ANANSE

      Public
      Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.
      grnkey-transcription-factorscell-fate-determinationenhancer-databasebioinformatics
      Python
      •
      MIT License
      •16•79•26•2•Updated Mar 6, 2024Mar 6, 2024

    • seq2science

      Public
      Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
      bioinformaticssnakemakepipelinereproducible-researchngsbioinformatics-pipelinefastqsrarna-seqchip-seq
      Python
      •
      MIT License
      •27•156•23•3•Updated Feb 5, 2024Feb 5, 2024

    • gimmemotifs

      Public
      Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.
      Python
      •
      MIT License
      •34•113•54•4•Updated Dec 19, 2023Dec 19, 2023

    • anansnake

      Public
      Automate long-running ANANSE analyses with snakemake
      Python
      •
      Apache License 2.0
      •1•1•2•1•Updated Nov 23, 2023Nov 23, 2023

    • scepia

      Public
      Single Cell Epigenome-based Inference of Activity
      Jupyter Notebook
      •
      MIT License
      •2•19•6•4•Updated Sep 27, 2023Sep 27, 2023

    • phylotypic_hourglass

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • seq2science-FAQ

      Public
      Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
      Python
      •
      MIT License
      •27•0•0•0•Updated Jun 22, 2023Jun 22, 2023

    • GroupMeetings

      Public
      HTML
      •2•0•0•0•Updated Mar 3, 2023Mar 3, 2023

    • ANANSE-CAGE

      Public
      Supporting scripts and notebooks detailing how to use ANANSE with CAGE data.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 7, 2022Dec 7, 2022

    • genomepy_manuscript

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jul 28, 2022Jul 28, 2022

    • seq2science-profiles

      Public
      Python
      •0•0•0•0•Updated Jun 23, 2022Jun 23, 2022

    • psap

      Public
      CLI interface for the PSAP classifier. PSAP implements a RandomForest approach to predict the probability of proteins to mediate protein phase separation (PPS)
      Python
      •
      MIT License
      •3•4•0•0•Updated May 10, 2022May 10, 2022

    • pytxi

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2022Apr 21, 2022

    • cfb_book

      Public
      Textbook for the Computation for Biologists course @ Radboud University
      Jupyter Notebook
      •0•2•0•0•Updated Oct 14, 2021Oct 14, 2021

    • aho_corasick

      Public
      fast motif scanning, but exploding memory
      Jupyter Notebook
      •0•0•0•0•Updated Jul 26, 2021Jul 26, 2021

    • Transcriptional_Burst_Kinetics

      Public
      Python
      •0•3•0•0•Updated Jun 14, 2021Jun 14, 2021

    • ANANSE-manuscript

      Public
      Notebook files describing analyses in the ANANSE paper (Xu et al. 2021)
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated May 26, 2021May 26, 2021

    • learnr.proto

      Public
      R
      •0•1•1•0•Updated Feb 23, 2021Feb 23, 2021

    • learnr.dashboard

      Public
      R
      •0•0•0•0•Updated Feb 5, 2021Feb 5, 2021

    • DevelopmentalRegulation_old

      Public
      living analysis, https://vanheeringen-lab.github.io/DevelopmentalRegulation/
      HTML
      •0•0•0•0•Updated Oct 2, 2020Oct 2, 2020

    • cfb_temp

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 2, 2020Oct 2, 2020

    • newproject

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 30, 2020Jun 30, 2020

    • peaksql

      Public
      Dynamic machine learning database for genomics.
      machine-learninggenomicsdataloader
      Python
      •
      MIT License
      •0•0•6•1•Updated May 26, 2020May 26, 2020

    • gimme-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 26, 2019Jul 26, 2019