Repositories list

• Anacapa

  Public
  Written by Emily Curd ([email protected]), Jesse Gomer ([email protected]), Gaurav Kandlikar ([email protected]), Zack Gold ([email protected]), Max Ogden ([email protected]), Lenore Pipes ([email protected])and Baochen Shi ([email protected]). Assistance was provided by Rachel Meyer ([email protected]).

  bioinformaticsednametabarcoding+ 2sequence-analysistaxonomic-analysis

  Python

  •

  MIT License

  •19•1•0•2•Updated Jul 24, 2024Jul 24, 2024

• t-rex-monitor

  Public
  T-REX job scheduler and metrics visualizer

  Shell

  •

  MIT License

  •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

• crux

  Public
  Pipeline For Creating eDNA Reference Libraries

  Shell

  •8•0•4•0•Updated Feb 20, 2024Feb 20, 2024

• taxid2taxonpath

  Public
  converts taxids to taxonpaths

  Python

  •2•0•0•0•Updated Jan 28, 2024Jan 28, 2024

• caledna

  Public
  Rails app that handles the data management flow for CALeDNA.

  Ruby

  •

  MIT License

  •0•2•0•46•Updated Jan 19, 2023Jan 19, 2023

• eDNA_Explorer

  Public
  Code repository for the ecoDASH project

  R

  •1•0•0•0•Updated Jul 11, 2022Jul 11, 2022

• POUR

  Public
  plantsdnaanimals+ 13fungibacteriaalgaebiodiversitymetabarcodingriverinvertebrates+ 6

  0•0•0•0•Updated Apr 30, 2021Apr 30, 2021

• caledna-squarespace

  Public
  Files for the CALeDNA Squarespace site

  Less

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

• trait-scripts

  Public
  assorted scripts related to species trait data

  Jupyter Notebook

  •1•0•0•0•Updated Oct 30, 2020Oct 30, 2020

• TaxonListToOpenTreePhylogeny

  Public
  This is a Jupyter Notebook to make phylogenetic trees with the Open Tree of Life from a list of taxa such as those from Anacapa output (CALeDNA format)

  jupyter-notebookphylogeneticsedna

  Jupyter Notebook

  •2•0•0•0•Updated Jun 17, 2020Jun 17, 2020

• eDNA-PCR-Project

  Public
  Raw and rarefied files for PCR Project

  1•0•0•0•Updated May 8, 2020May 8, 2020

• eDNA-metadata

  Public
  Jupyter Notebook

  •2•1•0•0•Updated Apr 2, 2020Apr 2, 2020

• ranacapa

  Public
  R package for downstream analysis for anacapa eDNA pipeline

  R

  •

  GNU General Public License v3.0

  •11•1•0•0•Updated Nov 8, 2019Nov 8, 2019

• Klamath-mountains

  Public
  Klamath mountains genus interaction data repository compatible with globalbioticinteractions.org

  22•1•0•0•Updated Jul 3, 2019Jul 3, 2019

• zeta-diversiy

  Public
  Analysis scripts using data from the CALeDNA consortium

  R

  •

  GNU General Public License v3.0

  •3•0•0•0•Updated May 20, 2019May 20, 2019