Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

Dirichlet process mixture of multivariate normal, skew normal or skew t-distributions modeling oriented towards flow-cytometry data preprocessing applications.


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Overview

NPflow is a package for performing Bayesian estimation of Dirichlet process mixtures of multivariate skew t-distributions. It is especially oriented towards flow-cytometry data preprocessing applications, but can be useful for numerous other applications.

The main function of the package is DPMpost().

The method implemented in this package is detailed in the following article:

Installation

The easiest way to get NPflow is to install it from CRAN:

install.packages("NPflow")

Or to get the development version from GitHub:

devtools::install_github("borishejblum/NPflow")

-- Boris Hejblum

News

News about the NPflow R package

Main changes in Version 0.13.1 (2017-08-02) --- this is only a minor release:

  • updated documentation and compiling standards

Main changes in Version 0.13.0 (2017-04-10):

  • use of itertools package for parallel computations
  • use of log-scale probabilities in slice-samplers for improved precision in computation
  • bug fix: parallel settings did not work in DPMpost (thanks to Mike Jiang for noticing this)
  • updated documentation

Main changes in Version 0.12.0 (2017-04-04) --- this is only a minor release:

  • registration of compiled functions
  • updated help and citation info

Main changes in Version 0.10.0 (2016-05-02):

  • optimization of the log-posterior computation for normal and skew normal distributions
  • improvement of the parallel sampler for normal distributions
  • added arguments in DPMGibs... functions to allow more informative priors if needed
  • bug fix: log of integers disambiguated in C++ function (compilation error on Solaris)

Reference manual

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install.packages("NPflow")

0.13.1 by Boris P. Hejblum, 7 months ago


Report a bug at https://github.com/borishejblum/NPflow/issues


Browse source code at https://github.com/cran/NPflow


Authors: Boris P. Hejblum [aut, cre], Chariff Alkhassim [aut], Francois Caron [aut]


Documentation:   PDF Manual  


LGPL-3 | file LICENSE license


Imports graphics, stats, grDevices, ellipse, fastcluster, gplots, ggplot2, pheatmap, reshape2

Depends on Rcpp, truncnorm

Suggests foreach, parallel, doParallel, itertools, microbenchmark

Linking to Rcpp, RcppArmadillo


See at CRAN