barmixR
This is the development version of barmixR; to use it, please install the devel version of Bioconductor.
Bayesian Modeling of Barcoded Tumor Mixtures for Quantitative Treatment Resistance Analysis
Bioconductor version: Development (3.24)
Implements the Bayesian modeling framework underlying the barmixR (BARcode MIXture analysis) platform for high-throughput quantitative analysis of genotype-specific treatment responses in pooled cancer cell populations. The package integrates barcode sequencing count data with volumetric measurements such as tumor volume (in vivo) or cellular confluency (in vitro) using hierarchical probabilistic models. Barcode counts are modeled with a Dirichlet–multinomial distribution to account for compositional sequencing data, while volumetric measurements are modeled using log-normal (tumor volume) or beta (confluency) likelihoods. Posterior inference is performed using Hamiltonian Monte Carlo through 'rstan'. The resulting posterior distributions enable estimation of clone-specific quantitative treatment resistance (QTR) together with uncertainty propagation from both sequencing and volumetric data. Additional functions provide posterior predictive checks, estimation of resistance ratios, treatment ranking, and visualization of resistance landscapes using violin plots and bubble heatmaps. The methods are designed for multiplexed lineage-tracing experiments in cancer research and were developed to analyze treatment resistance in gastrointestinal stromal tumors (GIST), but are broadly applicable to barcoding-based studies of treatment response and clonal dynamics across diverse cancer types.
Author: Mohammad Darbalaei [aut, cre]
, Daniel Hoffmann [aut]
, Barbara M. Grüner [ctb], Thomas Mühlenberg [ctb], Julia Zummack [ctb]
Maintainer: Mohammad Darbalaei <mohammad.darbalaei at uni-due.de>
citation("barmixR")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("barmixR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("barmixR")| barmixR: Bayesian Modeling of Barcoded Tumor Mixtures for Quantitative Treatment Resistance Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, Sequencing, Software, Visualization |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | utils, BiocParallel, dplyr, forcats, ggplot2, methods, patchwork, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.4.0), stats |
| System Requirements | GNU make, C++17, StanHeaders |
| URL | https://github.com/MohammadDarbalaei/barmixR |
| Bug Reports | https://github.com/MohammadDarbalaei/barmixR/issues |
See More
| Suggests | BiocStyle, knitr, MGLM, rmarkdown, testthat, tidyverse |
| Linking To | BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | barmixR_0.99.2.tar.gz |
| Windows Binary (x86_64) | barmixR_0.99.2.zip |
| macOS Binary (big-sur-x86_64) | barmixR_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | barmixR_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/barmixR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/barmixR |
| Bioc Package Browser | https://code.bioconductor.org/browse/barmixR/ |
| Package Short Url | https://bioconductor.org/packages/barmixR/ |
| Package Downloads Report | Download Stats |