Last updated: 2020-01-20

Checks: 1 1

Knit directory: 20170327_Psen2S4Ter_RNASeq/

This reproducible R Markdown analysis was created with workflowr (version 1.6.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Unstaged changes:
    Modified:   _workflowr.yml
    Modified:   analysis/QC.Rmd
    Modified:   analysis/_site.yml
    Modified:   analysis/about.Rmd
    Modified:   analysis/index.Rmd
    Modified:   data/samples.csv

Staged changes:
    New:        output/top30Overrepresented.fa
    New:        output/top30Overrepresented_BlastResults.txt

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd acb4f8a Steve Ped 2020-01-19 Start workflowr project.

Analysis of RNASeq data from the 3way comparison of WT zebrafish samples with Heterozygous mutants for psen2S4Ter and Homozygous mutants for psen2S4Ter. This mutant is expected to be a premature termination of the psen2 gene, but instead an alternate downstream start site resulted in a near full-length transcript with significant similarity to a conventional Early Onset Familial Alzhemier’s Disease mutation.

RNAseq was performed on total RNA with \(n=4\) samples in each group. Sequencing was performed by the sequencing facility at the Centre for Cancer Biology in Adelaide, using a NextSeq. Reads were provided in as paired-end, 150bp reads.

  1. Quality Assesment