Last updated: 2021-07-03

Checks: 2 0

Knit directory: wildlife-haemoprotozoa/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Repository version: 63bd5ef

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Ignored files:
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    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
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    Untracked:  data/NGS_18S_kinet/
    Untracked:  data/Sanger-piroplasm/
    Untracked:  data/haemoprotozoa.csv
    Untracked:  data/haemoprotozoa.xlsx
    Untracked:  data/tryp-phyloseq/count_data_QC.xlsx
    Untracked:  data/tryp-phyloseq/count_data_raw.csv
    Untracked:  data/tryp-phyloseq/sampledata.xlsx
    Untracked:  melt.csv
    Untracked:  melt.xlsx
    Untracked:  microscopy/
    Untracked:  output/plots/

Unstaged changes:
    Modified:   README.md
    Modified:   code/usearchv11_18S_Kineto.sh

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 63bd5ef siobhon-egan 2021-07-03 Formatting and setup updates
html 2d0d4fb siobhon-egan 2021-07-02 Build site.
Rmd cd30eb4 siobhon-egan 2021-07-02 update data vis page and remove wflow commands from index
html a36fbcb siobhon-egan 2021-07-02 Build site.
Rmd 8e3850e siobhon-egan 2021-07-02 Major update
html 9ad75d7 siobhon-egan 2021-03-18 Build site.
Rmd d429fdd siobhon-egan 2021-03-18 First publish
Rmd 4999de0 siobhon-egan 2021-02-12 Start workflowr project.

In the spirit of reproducibility this project website was created using workflowr package and outlines analysis performed for the following:

Egan, S., Taylor, C., Austen, J., Banks, P., Northover, A., Ahlstrom, L., Ryan, U., Irwin, P., and Oskam C. (Under review). Haemoprotozoa surveillance in peri-urban native and introduced wildlife.

Project website available here http://siobhonlegan.com/wildlife-haemoprotozoa/ and source code is available at https://github.com/siobhon-egan/wildlife-haemoprotozoa/

Data availability

Raw Illumina MiSeq data is available at European nucleotide archive under the project accession number PRJEB46031 (ERP130215), which includes the following sample accession numbers:

Nucleotide sequence data has been made available on Genbank, under the following accession numbers:

Supporting data

Data produced after bioinformatic analysis of raw Illumina MiSeq data such as taxonomy table, zOTU count data and metadata is available within the data/Rdata in .RData format.

Data used but not directly produced for this manuscript - nucleotide data generated for the molecular identification of ticks has been uploaded to GenBank under accession numbers MW665133–MW665150

Project website by Siobhon L. Egan, 2021. This site was created in R Markdown with workflowr