This repository contains software made available by JanBiotech to estimate cell counts from limited dilution assays.
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
showtext packages. I use the Myriad Pro fonts, users can substitute their own in the
font_add() function call in the
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
BayesQLD is still in development, check back for newer versions.