seqc provides quality control figures of cuffdiff results using the cummeRbund package. It produces a static HTML report. Optionally you can output the resulting figures separately.

• Installation
• Example
• Build Package
• Links & Additional Information
  • Make R aware of Bioconductor package dependencies
  • Credits

You can install the development version of seqc using:

# install.packages('devtools')
devtools::install_github("paulklemm/seqc")

Create a static HTML report based on a cuffdiff output and save all generated figures separately in the output_path.

library(seqc)
createHTMLReport(
  cuffdiff_path = '/beegfs/scratch/bruening_scratch/pklemm/htseq-tools-test/cuffdiff_output/TuUp',
  output_path = '/beegfs/scratch/bruening_scratch/pklemm/seqcOutput',
  save_plots = TRUE,
  save_width = 10,
  save_height = 10,
  save_format = 'pdf'
)

If you want to customize the image, download this repository, adapt the code and run the following code to build and install it.

roxygen2::roxygenise(); devtools::build(); devtools::install()

These information are not required for running the script and comprise lessons learned and hopefully useful information for fellow R users.

This tool relies on Bioconductor packages. To make R aware that some packages are to be downloaded from bioconductor you can use a trick of adding biocViews: in your DESCRIPTION file (see DESCRIPTION). This was described in this issue.

• This package adapts code provided by the cummeRbund Manual
• It also adapts code of the QC.R script of the mpg-age-bioinformatics htseq-tools