Repositories list

• schatzlab.github.io

  Public
  Source materials for schatzlab.github.io

  HTML

  •2•2•0•0•Updated Feb 2, 2025Feb 2, 2025

• panagram-data

  Public
  Data for panagram

  0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• jasmine-data

  Public
  Data for the jasmine project

  0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• appliedgenomics2024

  Public
  Materials for EN.601.449/649 Computational Genomics: Applied Comparative Genomics

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •3•3•0•0•Updated Dec 2, 2024Dec 2, 2024

• appliedgenomics2023

  Public
  Materials for EN.601.449/649 Computational Genomics: Applied Comparative Genomics

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •5•28•0•0•Updated Sep 9, 2024Sep 9, 2024

• genomescope

  Public
  Fast genome analysis from unassembled short reads

  JavaScript

  •

  Apache License 2.0

  •56•278•81•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•6•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•21•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•78•0•0•Updated Jan 29, 2019Jan 29, 2019

• datastructures2018

  Public
  Materials for JHU Data Structures 2018

  Java

  •13•18•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•57•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