ddpcRquant: threshold determination and automation of single channel droplet digital PCR experiments

Installing and using ddpcRquant

Requirements for ddpcRquant:

• R installation, R version >= 3.1.1: download link here
• Rstudio installation: download link here

Using ddpcRquant by script:

• The download for the ddpcRquant functions (QX100): ddpcrquant_functions_qx100.R

• The download for the ddpcRquant functions (QX200): ddpcrquant_functions_qx200.R

• The download for the instructions script: ddpcrquant_guide.R
  

=> Open ddpcrquant_guide.R in Rstudio and folllow the instructions

Using ddpcRquant by webbased tool:

• version available at: ddpcrquant webtool link
• version available at: ddpcrquant webtool link (old)

=> Might not work via eduroam internet access

• version available as shiny package:ddpcrquant_shiny.zip

=> Unzip and run as Shiny App in RStudio: select "external" for webbased use

Supported platforms and on-demand features

• Currently BioRad QX100 and QX200 are compatible with ddpcRquant, for use with the Stilla Naica or other platforms please contact: Wim.Trypsteen@ugent.be
• For access to the multirun analysis mode, please contact: Wim.Trypsteen@ugent.be
• A new ddpcRquant update will come out 2022 that will include above-mentioned features

Please cite:

Trypsteen et al. ddpcRquant: threshold determination for single channel droplet digital PCR experiments. Anal Bioanal Chem. 2015 Jul;407(19):5827-34. (PMID:26022094)

Find full text: Pubmed or ResearchGate

First analysis with ddpcRquant

• Test dataset (QX100) is available here: test

=> The expected output with full automatisation can be found per assay (reps=10,threshold=0.995): assay1: RnaseP assay2: RU5

• Contact information for reporting problems or questions concerning analysis: wim.trypsteen@ugent.be

Course digital PCR (22/11/18, Ghent, Belgium)

• course slides are available here: course

• Exercises folder is available here: exercises

Doctoral schools ddPCR (01/09/16, Ghent, Belgium)

• ddpcrquant course slides are available here: course

• Exercises folder is available here: exercises

• ddpcrquant solution to exercises: ddpcrquant solution exercises

• ddpcrquant quick analysis guide available here: ddpcrquant quick analysis guide

• Contact information: wim.trypsteen@ugent.be

Slides Master Bioinformatics (28/11/19, Ghent, Belgium)

• slides available here: hands-on slides

Summer Course Exercise Dataset (24/09/15, Ghent, Belgium)

• Exercise dataset (QX100) is available here: exercise_testfiles

• ddpcrquant course slides (theory + concepts) are available here: ddpcrquant course

• ddpcrquant hands-on slides (how to guide) are available here: ddpcrquant handson

• Contact information: wim.trypsteen@ugent.be