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    28 repositories

    • cmdb-quantbio

      Public
      Materials for Fall 2023 CMDB Quantitative Biology Bootcamp and Lab
      Jupyter Notebook
      •0•3•0•0•Updated Nov 22, 2024Nov 22, 2024

    • qbb2024

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • bx-python

      Public
      Tools for manipulating biological data, particularly multiple sequence alignments
      Python
      •
      MIT License
      •54•150•16•3•Updated Sep 15, 2024Sep 15, 2024

    • hifive

      Public
      Tools for handling HiC and 5C data
      Python
      •
      MIT License
      •8•23•7•0•Updated Feb 5, 2024Feb 5, 2024

    • cmdb-laptop-setup

      Public
      Basic web and app developer Mac setup in Ansible playbooks.
      Shell
      •
      Other
      •1.8k•0•0•0•Updated Nov 7, 2023Nov 7, 2023

    • metaWRAP

      Public
      MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
      Shell
      •
      MIT License
      •190•403•479•7•Updated Jul 28, 2023Jul 28, 2023

    • 2018.09.01_Eldred_GWAS

      Public
      Python
      •0•0•0•0•Updated Dec 13, 2022Dec 13, 2022

    • cmdb-quantbio-prepwork

      Public
      CSS
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Sep 16, 2022Sep 16, 2022

    • cmdb-plot-vcfs

      Public
      Shell
      •0•0•0•0•Updated Aug 30, 2022Aug 30, 2022

    • qbb2021

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Oct 22, 2021Oct 22, 2021

    • qbb2020

      Public
      Jupyter Notebook
      •3•0•0•0•Updated Oct 9, 2020Oct 9, 2020

    • cmdb-laptop-setup_windows

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Aug 26, 2020Aug 26, 2020

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Perl
      •186•0•0•0•Updated Jun 22, 2020Jun 22, 2020

    • PHOSforUS

      Public
      Github repository for PHOSforUS predictor distribution
      Python
      •
      MIT License
      •1•0•0•0•Updated May 26, 2020May 26, 2020

    • timeline_paper

      Public
      Files associated the halite longitudinal analysis manuscript
      HTML
      •1•3•0•0•Updated Sep 4, 2019Sep 4, 2019

    • metawrap_paper

      Public
      All data associated with writing the metaWRAP paper - data files, figure-making scripts, figures, and manuscript drafts
      HTML
      •2•0•0•0•Updated Dec 4, 2018Dec 4, 2018

    • paper-2016.12-anderson-elife

      Public
      Methods supporting https://doi.org/10.7554/eLife.29593.001
      R
      •
      MIT License
      •1•0•0•0•Updated Mar 12, 2018Mar 12, 2018

    • Quasar_Paper

      Public
      TeX
      •3•0•0•0•Updated Oct 17, 2017Oct 17, 2017

    • Quasar_PaperAnalysis

      Public
      All scripts and information needed to perform all analyses and generate all figures from the HiFive QuASAR paper.
      Python
      •0•0•0•0•Updated Oct 16, 2017Oct 16, 2017

    • LADetector

      Public
      LADetector package and scripts
      Perl
      •4•0•0•0•Updated Oct 3, 2017Oct 3, 2017

    • galaxy-hackathon

      Public
      Data intensive science for everyone.
      Python
      •
      Other
      •1k•7•46•2•Updated Jun 27, 2017Jun 27, 2017

    • galaxy_hic_database

      Public
      A HiC database of chromatin interaction data from mapped, paired reads, HiFive multi-resolution heatmaps, and everything in between.
      HTML
      •1•0•0•0•Updated Oct 27, 2015Oct 27, 2015

    • HiFive_Paper

      Public
      All of the scripts necessary to produce the analyses performed in the HiFive paper.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Sep 14, 2015Sep 14, 2015

    • esperr-examples

      Public
      Examples for running ESPERR to produce Regulatory Potential (RP) scores
      Makefile
      •0•0•0•0•Updated Jun 23, 2015Jun 23, 2015

    • esperr-genomeresearch-2006

      Public
      Code and examples for ESPERR paper (Taylor et al. 2006, Genome Research)
      Python
      •0•0•0•0•Updated Jun 23, 2015Jun 23, 2015

    • esperr

      Public
      Code for ESPERR (Evolutionary and Sequence Pattern Extraction through Reduced Representation)
      Python
      •1•0•0•0•Updated Jun 23, 2015Jun 23, 2015

    • class-ibs-796-fall2013

      Public
      Python
      •1•1•0•0•Updated Nov 9, 2013Nov 9, 2013

    • class-ibs-796-fall2013-playground

      Public
      11•0•0•0•Updated Sep 4, 2013Sep 4, 2013