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    32 repositories

    • appliedgenomics2024

      Public
      Materials for EN.601.449/649 Computational Genomics: Applied Comparative Genomics
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•2•0•0•Updated Nov 6, 2024Nov 6, 2024

    • schatzlab.github.io

      Public
      Source materials for schatzlab.github.io
      HTML
      •2•2•0•0•Updated Oct 7, 2024Oct 7, 2024

    • appliedgenomics2023

      Public
      Materials for EN.601.449/649 Computational Genomics: Applied Comparative Genomics
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •5•27•0•0•Updated Sep 9, 2024Sep 9, 2024

    • genomescope

      Public
      Fast genome analysis from unassembled short reads
      JavaScript
      •
      Apache License 2.0
      •57•258•78•4•Updated Apr 8, 2024Apr 8, 2024

    • PodPlot

      Public
      Plot coverage or percent of total sequence as a function of minimum read length
      Python
      •3•5•1•0•Updated Mar 21, 2024Mar 21, 2024

    • wdl101-2023

      Public
      wdl101 2023 edition
      MIT License
      •0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

    • t2t-chm13-chry

      Public
      Jupyter Notebook
      •0•9•0•0•Updated Jul 9, 2023Jul 9, 2023

    • appliedgenomics2022

      Public
      Materials for EN.601.449/EN.601.649 Computational Genomics: Applied Comparative Genomics
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •9•23•0•0•Updated Dec 8, 2022Dec 8, 2022

    • long-read-commentary

      Public
      R
      •0•0•0•0•Updated Dec 1, 2022Dec 1, 2022

    • t2t-variants

      Public
      Papyrus
      •
      MIT License
      •6•20•3•0•Updated Aug 8, 2022Aug 8, 2022

    • Col-CEN

      Public
      Resources for the Col-CEN reference genome assemblies
      3•11•10•0•Updated Feb 15, 2022Feb 15, 2022

    • anvil

      Public
      MIT License
      •0•1•0•0•Updated Jan 18, 2022Jan 18, 2022

    • biomedicalresearch2021

      Public
      Course Materials for EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research
      Creative Commons Zero v1.0 Universal
      •3•13•0•0•Updated Nov 29, 2021Nov 29, 2021

    • appliedgenomics2021

      Public
      Materials for Spring 2021 Applied Genomics Course
      9•52•0•0•Updated Apr 21, 2021Apr 21, 2021

    • coursetest

      Public
      testing course management
      MIT License
      •0•0•0•0•Updated Mar 16, 2021Mar 16, 2021

    • iGenomics-data

      Public
      Test data for iGenomics
      MIT License
      •0•0•1•0•Updated Oct 29, 2020Oct 29, 2020

    • LongTron

      Public
      Shell
      •
      Apache License 2.0
      •2•2•0•0•Updated Oct 26, 2020Oct 26, 2020

    • appliedgenomics2020

      Public
      Description Materials for Spring 2020 Applied Genomics Course
      Jupyter Notebook
      •4•16•0•0•Updated Apr 22, 2020Apr 22, 2020

    • crossstitch

      Public
      Code for phasing SVs with SNPs
      Java
      •3•52•8•0•Updated Mar 27, 2020Mar 27, 2020

    • biomedicalresearch2019

      Public
      Course Materials for EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research
      Python
      •1•0•0•0•Updated Dec 2, 2019Dec 2, 2019

    • pseudohaploid

      Public
      Create a pseudohaploid assembly from a partially resolved diploid assembly
      Perl
      •5•32•2•0•Updated Nov 22, 2019Nov 22, 2019

    • Nchart

      Public
      Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file
      R
      •5•0•0•0•Updated Apr 30, 2019Apr 30, 2019

    • appliedgenomics2019

      Public
      Materials for Spring 2019 Applied Genomics Course
      8•21•0•0•Updated Apr 22, 2019Apr 22, 2019

    • appliedgenomics2018

      Public
      Materials for Spring 2018 Applied Genomics Course
      Jupyter Notebook
      •30•77•0•0•Updated Jan 29, 2019Jan 29, 2019

    • datastructures2018

      Public
      Materials for JHU Data Structures 2018
      Java
      •13•17•0•0•Updated Dec 11, 2018Dec 11, 2018

    • biomedicalresearch2017

      Public
      EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research
      Jupyter Notebook
      •
      MIT License
      •3•3•0•0•Updated Dec 3, 2018Dec 3, 2018

    • appliedgenomics2017

      Public
      JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
      HTML
      •
      MIT License
      •14•56•0•0•Updated Mar 8, 2018Mar 8, 2018

    • scikit-ribo_manuscript

      Public
      Reproducing the analysis in the scikit-ribo manuscript using iPython notebooks
      Jupyter Notebook
      •2•1•0•0•Updated Sep 11, 2017Sep 11, 2017

    • scikit-ribo

      Public
      Accurate estimation and robust modelling of translation dynamics at codon resolution
      random-forestglmnetglmridge-regressionriboseq
      Python
      •
      GNU General Public License v2.0
      •8•18•6•0•Updated Jun 27, 2017Jun 27, 2017

    • GECCO

      Public
      Genomic Enrichment Computational Clustering Operation
      Python
      •0•0•0•0•Updated Jun 20, 2017Jun 20, 2017