Primer scripts to produce meaningful visualisations from pre-processed metabarcoding data
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Updated
Jul 13, 2023 - R
Primer scripts to produce meaningful visualisations from pre-processed metabarcoding data
Data & Code Supplement for "Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems"
Supplementary files for the paper "Environmental DNA metabarcoding of Danish soil samples reveals new insight into the hidden diversity of eutardigrades in Denmark"
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)
A set of functions for filtering erroneous sequences in eDNA metabarcoding data
Supporting codes for Manu et al., Ecological Indicators (2023). Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems
In this research project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.
"An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies"
Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
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
website of the otterconnect project
Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)
A collection of singularity recipies for bioinformatic pipelines.
Environmental DNA reflects common mitochondrial haplotypic variation
repository of data examples for the R package metabaR
Official GitHub repository for the R package "Species Identity and Evolution in R" (spider)
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