Title: Shrinking Characteristics of Precision Matrix Estimators
Description: Estimates a penalized precision matrix via an augmented ADMM algorithm. This package is an implementation of the methods described in "Shrinking Characteristics of Precision Matrix Estimators" by Aaron J. Molstad, PhD and Adam J. Rothman, PhD. The manuscript can be found here: <doi:10.1093/biomet/asy023> .
Suggests: testthat, knitr, rmarkdown, microbenchmark, glasso, pkgdown

Title: Impute Single-Cell RNA-Seq Data Method
Description: It aims to impute drop-out data by optimizing an objective function
that consists of three terms. The first term ensures that imputed values for
genes with nonzero expression remain as close to their original values as possible,
thus minimizing unwanted bias towards expressed genes. The second term ensures the
rank of the imputed data matrix to be as small as possible. The rationale is that
we only expect a limited number of distinct cell types in the samples. The third term
operates on the bulk RNA-Seq data. It ensures consistency between the average gene
expression of the aggregated imputed data and the average gene expression of the bulk
RNA-Seq data. We developed a convex optimization algorithm to minimize the objective function.
Imports: Rcpp (>= 0.12.13), rARPACK, pracma, ggplot2, RColorBrewer,

Title: An Accurate Simulator for Single-Cell RNA Sequencing Data
Authors@R: person("Fei", "Qin", role = c("aut", "cre", "cph"), email = "fqin@email.sc.edu")
Description: We provide a comprehensive scheme that is capable of simulating Single Cell RNA Sequencing data for various parameters of Biological Coefficient of Variation,
busting kinetics, differential expression (DE), cell or sample groups, cell trajectory, batch effect and other experimental designs.
'SCRIP' proposed and compared two frameworks with Gamma-Poisson and Beta-Gamma-Poisson models for simulating Single Cell RNA Sequencing data.
Other reference is available in Zappia et al. (2017) <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1305-0>.
1.14.1), edgeR(>= 3.34.0), methods, stats, mgcv, knitr,
BiocManager, BiocGenerics, Seurat, crayon, fitdistrplus,