walterxie/edna-pipeline

eDNA pipeline

eDNA-pipeline

This is the page for developers, users please go to http://walterxie.github.io/eDNA-pipeline/

The available projects are:

Methods

DNA extraction and PCR replication comparison from one site (i.e. the second Waitakere samples experiment).

Citation

Andrew Dopheide, Dong Xie, Thomas R. Buckley, Alexei J. Drummond, and Richard D. Newcomb. (2018), Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity, in review.

Source

R code is available at http://github.com/andrewdopheide/DNA_extr_PCR_impacts

LBI Hauturu

Citation

Andrew Dopheide, Dong Xie, Laura Ward, Nicola Nelson, Thomas R Buckley, Alexei J Drummond, and Richard D Newcomb, (2018): Simultaneous DNA meta-barcoding analysis of soil prokaryotes and eukaryotes in a forested island ecosystem reveals contrasting patterns of biodiversity, in review.

Source

Branch hauturu: http://github.com/walterxie/eDNA-pipeline/tree/hauturu

The code is depended on ComMA package.

LBI pilot

Citation

Alexei J Drummond, Richard D Newcomb, Thomas R Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A Ross, Leah Tooman, Stefanie Grosser, Duckchul Park, Nicholas J Demetras, Mark I Stevens, James C Russell, Sandra H Anderson, Anna Carter and Nicola Nelson, (2015): Evaluating a multigene environmental DNA approach for biodiversity assessment, GigaScience.

The online version of this article (doi:10.1186/s13742-015-0086-1) or http://link.springer.com/article/10.1186/s13742-015-0086-1

Supporting data in GigaScience Database: http://dx.doi.org/10.5524/100144

Source

Branch pilot: http://github.com/walterxie/eDNA-pipeline/tree/pilot

edna-pipeline's Issues

implement Dynamic Documents

http://rmarkdown.rstudio.com