Repositories list

• dam_mutagensis_chemistry

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

• bcmb_bootcamp

  Public
  Repo for BCMB Computational Bootcamp Course

  Jupyter Notebook

  •15•2•0•0•Updated Sep 2, 2024Sep 2, 2024

• grossman_prolificans

  Public
  genome assembly of Lomentospora prolificans

  Shell

  •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

• fan_methylation_binning

  Public
  Code used for methylation binning paper

  R

  •0•0•0•0•Updated Apr 14, 2024Apr 14, 2024

• Zuniga_Aikin_2024_ERK

  Public
  Code for processing of RNA-seq data from "Sustained ERK Signaling Promotes G2 Cell Cycle Exit and primes cells for Whole Genome Duplication" Zuniga, Aikin, et al. (2024)

  Shell

  •

  MIT License

  •0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• tague_splitcre

  Public
  All code for preprocessing sequencing data for split cre screen

  Shell

  •0•0•0•0•Updated May 3, 2023May 3, 2023

• nanoNOMe

  Public
  nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis

  Python

  •5•18•1•0•Updated Nov 18, 2022Nov 18, 2022

• hg002_chrY_methylation

  Public
  Code for analysis of methylation on HG002 chrY

  Python

  •0•0•0•0•Updated Oct 25, 2022Oct 25, 2022

• Telomere_Length

  Public
  This repository contains the pipeline for assessing telomere length from "Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing"

  R

  •1•5•0•0•Updated Feb 8, 2022Feb 8, 2022

• Drug_resistant_GBM

  Public
  FLAIR and SUPPA2 analysis for "Targeting destabilized DNA g-quadruplexes and aberrant splicing in amyloid-like aggregate positive drug-resistant glioblastoma"

  Jupyter Notebook

  •1•0•0•0•Updated Feb 2, 2022Feb 2, 2022

• T2T-Epigenetics

  Public
  Repository for analysis scripts for the T2T Epigenetics manuscript

  HTML

  •1•7•1•0•Updated Jan 28, 2022Jan 28, 2022

• Yeast-Telomere-Nanopore

  Public
  Telomere length measurement

  0•1•0•0•Updated Jun 1, 2021Jun 1, 2021

• yeh_sinv

  Public
  Sequencing analysis for Yeh et al paper

  R

  •

  MIT License

  •0•0•0•0•Updated Jun 1, 2021Jun 1, 2021

• ambic-epigenome

  Public
  AMBIC Epigenomics project analysis

  Jupyter Notebook

  •

  MIT License

  •2•1•0•0•Updated Apr 21, 2021Apr 21, 2021

• chm13_meth

  Public
  Methylation analysis of chrx in chm13 assembly

  HTML

  •0•1•0•0•Updated Apr 13, 2021Apr 13, 2021

• nivar

  Public
  analysis for C. nivariensis asm paper

  R

  •1•0•0•0•Updated Mar 29, 2021Mar 29, 2021

• jhu-covid-pipeline

  Public
  Viral Genomics Pipeline in use at JHU

  Shell

  •0•3•0•0•Updated Mar 1, 2021Mar 1, 2021

• nanopore-methylation-utilities

  Public
  Python

  •9•29•2•0•Updated Feb 5, 2021Feb 5, 2021

• ncov

  Public
  ncov work

  Shell

  •0•2•0•0•Updated Jan 28, 2021Jan 28, 2021

• cpowgs_r21

  Public
  Code/scripts involvign cpowgs R21 grant

  HTML

  •0•0•0•0•Updated Dec 29, 2020Dec 29, 2020

• vremanu

  Public
  Code for VRE sequencing manuscript

  HTML

  •1•0•0•0•Updated Oct 10, 2020Oct 10, 2020

• moth

  Public
  HTML

  •0•0•0•0•Updated Sep 1, 2020Sep 1, 2020

• Cas9Enrichment

  Public
  scripts for analysis associated with Cas9Enrichment publication

  Shell

  •2•12•0•0•Updated Feb 10, 2020Feb 10, 2020

• drewes_fmt

  Public
  Analysis scripts for JCI Insight paper

  Shell

  •0•0•0•0•Updated Sep 18, 2019Sep 18, 2019

• hummingbird

  Public
  Shell

  •

  MIT License

  •3•3•1•0•Updated Jul 31, 2019Jul 31, 2019

• rna_consortia

  Public
  Nanopore RNA consortia data and analysis

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated May 25, 2019May 25, 2019

• fragillis

  Public
  Code for analysis of fragillis toxin project

  R

  •1•0•0•1•Updated Dec 2, 2018Dec 2, 2018

• chicken

  Public
  R

  •4•0•0•0•Updated Aug 9, 2018Aug 9, 2018

• timp_oxa

  Public
  Scripts for oxa paper analysis

  R

  •0•0•0•0•Updated Aug 7, 2018Aug 7, 2018

• timp_illumina

  Public
  R

  •0•0•0•0•Updated Nov 8, 2017Nov 8, 2017