Repositories list

• UTwastewaterARG

  Public
  Identification of ARGs and MGEs in wastewater metagenomes

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• lab_scripts

  Public
  Standalone scripts used in the lab's various bioinformatics workflows

  Python

  •

  GNU General Public License v2.0

  •2•7•7•0•Updated Oct 7, 2023Oct 7, 2023

• Lost-City-MutY-Discovery

  Public
  R

  •2•0•0•0•Updated Jan 18, 2023Jan 18, 2023

• Brazelton-2022-Lost-City-fluids-MAGs

  Public
  Supplemental files associated with Brazelton et al. manuscript on Lost City fluids MAGs

  HTML

  •

  MIT License

  •0•0•0•0•Updated Sep 13, 2022Sep 13, 2022

• Briggs_Methanosarcinales

  Public
  0•0•0•0•Updated Feb 10, 2022Feb 10, 2022

• Dangerfield-2020-PeerJ

  Public
  Supplemental data associated with Dangerfield et al. 2020 https://peerj.com/articles/9307/

  HTML

  •0•0•0•0•Updated Dec 21, 2021Dec 21, 2021

• Brazelton-2017-PeerJ

  Public
  Supplemental data associated with Brazelton et al. (2017) PeerJ

  HTML

  •0•0•0•0•Updated Nov 27, 2021Nov 27, 2021

• Pendleton-2021-Sci-Drill

  Public
  Supplemental data associated with Pendleton et al. 2021 Scientific Drilling

  0•0•0•0•Updated Nov 27, 2021Nov 27, 2021

• protocols

  Public
  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 17, 2021Nov 17, 2021

• McGonigle-2019-LCY

  Public
  Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems

  0•0•0•0•Updated Nov 16, 2021Nov 16, 2021

• Thornton_2020

  Public
  Scripts and R-code used in Thornton et al., 2020

  Shell

  •0•0•0•0•Updated Nov 16, 2021Nov 16, 2021

• McGonigle-BSF-Metagenome-2021

  Public
  Supplement for Metabolic Potential of Microbial Communities in the Hypersaline Sediments of the Bonneville Salt Flats

  0•0•0•0•Updated Nov 16, 2021Nov 16, 2021

• bio_utils

  Public
  Python package containing modules of commonly used bioinformatic scripts

  Python

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Nov 16, 2021Nov 16, 2021

• seq-annot

  Public
  Tools to facilitate annotation and comparison of genomes and metagenomes

  Python

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Mar 5, 2021Mar 5, 2021

• module_files

  Public
  Module Files used on our cluster

  Roff

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 14, 2020Feb 14, 2020

• Atlantis-Massif-2015

  Public
  Materials associated with Motamedi et al. (2019)

  0•0•0•0•Updated Dec 9, 2019Dec 9, 2019

• seq-qc

  Public
  Basic tools for preprocessing sequencing reads

  Python

  •

  GNU General Public License v2.0

  •0•0•2•0•Updated Oct 7, 2019Oct 7, 2019

• Atlantis-Massif-2015-paper

  Public
  0•0•0•0•Updated Oct 4, 2019Oct 4, 2019

• McGonigle-2019

  Public
  0•0•0•0•Updated May 14, 2019May 14, 2019

• system

  Public
  Python

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Aug 15, 2018Aug 15, 2018

• oak

  Public
  Ontological Annotation using Kegg

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 4, 2017Nov 4, 2017

• jarvis

  Public
  jarvis

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Aug 14, 2017Aug 14, 2017

• Dangerfield-2017

  Public
  Protocols and software associated with Dangerfield et al. 2017 "Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest"

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 14, 2017Jul 14, 2017

• metameta

  Public
  Software suite for analyzing metatranscriptome data mapped onto metagenomic data

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 20, 2016Dec 20, 2016