Description: Bisulfite-treated RNA non-conversion in a set of samples is
analysed as follows : each sample's non-conversion distribution is
identified to a Poisson distribution. P-values adjusted for multiple
testing are calculated in each sample. Combined non-conversion P-values
and standard errors are calculated on the intersection of the set of
samples. For further details, see C Legrand, F Tuorto, M Hartmann,
R Liebers, D Jakob, M Helm and F Lyko (2017) <doi:10.1101/gr.210666.116>.

Title: Decomposition of Bulk Expression with Single-Cell Sequencing
person(given = 'Brandon', family = 'Jew', email = 'brandon.jew@ucla.edu', role = c('aut', 'cre')),
person(given = 'Marcus', family = 'Alvarez', role = 'aut')
Description: Provides tools to accurately estimate cell type abundances
from heterogeneous bulk expression. A reference-based method utilizes
single-cell information to generate a signature matrix and transformation
of bulk expression for accurate regression based estimates. A marker-based
method utilizes known cell-specific marker genes to measure relative
For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.
Suggests: Seurat, plyr, knitr, rmarkdown, testthat

Imports: Biobase, limSolve, methods, stats

Title: Basu-Dhar Bivariate Geometric Distribution
Author: Ricardo Puziol de Oliveira and Jorge Alberto Achcar
Maintainer: Ricardo Puziol de Oliveira <rpuziol.oliveira@gmail.com>
Description: Computes the joint probability mass function, the joint cumulative distribution, the correlation coefficient and generate random deviates from the Basu-Dhar bivariate geometric distribution. The package also computes the joint survival function in presence of cure fraction using the mixture model approach (For more details, see Achcar et. al (2016) <doi:10.1080/02664763.2015.1117589> and de Oliveira et. al (2018) <doi:10.1080/02664763.2018.1495701>).

Description: Computes the joint probability mass function (pmf), the joint cumulative function (cdf), the joint survival function (sf), the correlation coefficient, the covariance, the cross-factorial moment and generate random deviates for the Basu-Dhar bivariate geometric distribution as well the joint probability mass, cumulative and survival function assuming the presence of a cure fraction given by the standard bivariate mixture cure fraction model. The package also computes the estimators based on the method of moments.
URL: For more details, see de Oliveira et. al (2018)