This repository contains software made available by JanBiotech to estimate cell counts from limited dilution assays.

Simulations

The simulation folder contains the R code for simulating such assays and plotting the results. Running these simulations trains intuition and provides the ground truth for testing of model implementations. The simulations currently implemented follow the protocol of the QVOA assay to estimate the latent reservoir of replication competent HIV. The scripts depend on the data.table R package. Plotting depends on ggplot2 and showtext packages. I use the Myriad Pro fonts, users can substitute their own in the font_add() function call in the simPlots.Rnw script.

Quantal dilution assay analyses

The R package for Bayesian analyses of quantal dilution assays (such as QVOA) is in the BayesQLD directory of this repository. It depends only on Rcpp. It can be installed directly from GitHub by running install_github("JanBiotech/BayesLiDiCal/BayesQLD"), which requires the devtools package.

BayesQLD is still in development, check back for newer versions.