Repositories list

• Harper_et_al_2020_mustelid_diet_metabarcoding

  Public
  R

  •0•1•0•0•Updated Nov 20, 2020Nov 20, 2020

• Harper_et_al_2018_mammal_eDNA_metabarcoding

  Public
  R

  •1•0•0•0•Updated Oct 21, 2020Oct 21, 2020

• Harper_et_al_2018

  Public
  Jupyter Notebook

  •1•2•1•0•Updated Oct 21, 2020Oct 21, 2020

• Harper_et_al_2020_crucian_carp_impact_invertebrates_conventional_molecular_tools

  Public
  R

  •1•1•0•0•Updated Oct 21, 2020Oct 21, 2020

• Griffiths_et_al_2020_Fens_eDNA

  Public
  Data processing workflow and supplementary info for: Griffiths et al. (2020) - Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments

  R

  •0•2•0•0•Updated Jul 19, 2020Jul 19, 2020

• Curated_reference_databases

  Public
  This repository contains the complete description of how we produced the curated reference databases for the studies in Evolutionary and Environmental Genomics Group (@EvoHull)

  reference-database12scytb

  HTML

  •2•2•0•0•Updated Jun 27, 2019Jun 27, 2019

• Li_et_al_2019_eDNA_dynamic

  Public
  Data processing workflow and supplementary data for Li et al. 2019 - Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

  R

  •0•0•0•0•Updated Jun 27, 2019Jun 27, 2019

• Handley_et_al_2019

  Public
  Data processing workflow and supplementary data for Handley et al. 2019 - Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake

  workflowillumina-datataxonomic-assignment

  Jupyter Notebook

  •0•1•1•0•Updated Jun 5, 2019Jun 5, 2019

• Li_et_al_2019_eDNA_fish_monitoring

  Public
  Data processing workflow and supplementary data for Li et al. 2019 - Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes

  lakesednametabarcoding

  R

  •0•3•0•0•Updated Jun 5, 2019Jun 5, 2019

• metaBEAT

  Public
  Metabarcoding analyses pipeline - metaBarcoding and Environmental DNA Analysis Tool

  Python

  •3•19•1•1•Updated Apr 17, 2019Apr 17, 2019

• HullUni-bioinformatics.github.io

  Public
  CSS

  •0•2•0•0•Updated Feb 26, 2019Feb 26, 2019

• Dockerize

  Public
  This repository contains contexts for Docker images build for miscellaneous pieces of bioinformatics software.

  Shell

  •0•1•0•0•Updated Jan 16, 2019Jan 16, 2019

• Li_et_al_2018_eDNA_filtration

  Public
  Data processing workflow and supplementary data for Li et al. 2018 - The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding

  ednaworkflowfiltration+ 2supplementary-dataillumina-data

  R

  •1•0•0•0•Updated May 16, 2018May 16, 2018

• MIG-Phylogenomics

  Public
  MIG Meloidogyne species phylogenomics and and ploidy analysis

  Python

  •3•5•0•0•Updated Feb 21, 2018Feb 21, 2018

• Kitson_et_al_NMB

  Public
  Repository contains scripts and supplementary data for Kitson et al. - Nested metabarcoding manuscript

  HTML

  •0•0•0•0•Updated Feb 2, 2018Feb 2, 2018

• Diplotaxodon_twilight_RAD

  Public
  Data repository accompanying the paper 'The genomic basis of cichlid fish adaptation within the deep water 'twilight zone' of Lake Malawi' by Hahn et al.

  Jupyter Notebook

  •1•0•0•0•Updated Jul 31, 2017Jul 31, 2017

• Blackman_et_al_Gfossarum_UK

  Public
  Data processing workflow and supplementary data for Blackman et al. - First record of GAMMARUS FOSSARUM (Koch, 1836) (AMPHIPODA, GAMMARIDEA) in the UK - a new non-native species discovered using Environmental DNA

  UnrealScript

  •0•0•0•0•Updated Apr 5, 2017Apr 5, 2017

• egrep-2016

  Public
  Repository for course 'Environmental Genomics Research Projects (egrep)' 2016 @EvoHull

  teaching

  HTML

  •0•1•0•0•Updated Sep 30, 2016Sep 30, 2016

• metabarcode-course-2016

  Public
  Data for 'Reproducible metabarcoding course' 2016 @EvoHull

  HTML

  •1•1•0•0•Updated Sep 14, 2016Sep 14, 2016

• Nematoda-TE-Evolution

  Public
  Analysis for the paper "Genetic drift, not life history or RNAi, determine long term evolution of transposable elements"

  Jupyter Notebook

  •5•8•0•0•Updated Sep 14, 2016Sep 14, 2016

• TE-search-tools

  Public
  Python wrappers for programs that search for transposable elements

  Jupyter Notebook

  •6•19•0•0•Updated Jul 12, 2016Jul 12, 2016

• genomisc-training

  Public
  Miscellaneous materials (tutorials, exercises, testdata) to develop essential 'survival'-skills in bioinformatics.

  MIT License

  •1•5•0•0•Updated Jul 4, 2016Jul 4, 2016

• ReproPhylo

  Public
  Reproducible Phylogenomics

  Jupyter Notebook

  •4•22•24•0•Updated Jun 28, 2016Jun 28, 2016

• Haenfling_et_al_2016

  Public
  Data processing workflow and supplementary data for Haenfling et al. 2016 - Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

  R

  •5•6•1•0•Updated Jun 22, 2016Jun 22, 2016

• misc

  Public
  General use python objects

  Jupyter Notebook

  •0•0•0•0•Updated May 8, 2016May 8, 2016

• ReproPhyloDockerfile

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •0•4•0•0•Updated Jan 10, 2016Jan 10, 2016

• egrep

  Public
  Repository for course 'Environmental Genomics Research Projects (egrep)'

  teaching

  HTML

  •0•0•0•0•Updated Oct 1, 2015Oct 1, 2015

• metabarcode-course

  Public
  EvoHull bioinformatics and metabarcoding repository

  teachingdockermetabarcode-course

  HTML

  •1•2•0•0•Updated Jun 10, 2015Jun 10, 2015

• Your-Species-In-GenBank

  Public
  2•1•0•0•Updated May 29, 2015May 29, 2015

• ReproPhyloGalaxy

  Public
  A Galaxy instance with ReproPhylo tools

  Python

  •1•3•0•0•Updated Dec 4, 2014Dec 4, 2014