Packaged: 2021-05-08 14:46:09 UTC; Weksi Budiaji

Title: Diagonally Dominant Principal Component Analysis
Author: Zheng Tracy Ke <zke@fas.harvard.edu>
Description: Consider the problem of decomposing a large covariance matrix into a low rank matrix plus a diagonally dominant matrix. This problem is called Diagonally Dominant Principal Component Analysis (DD-PCA) in the reference Ke, Z., Xue, L. and Yang, F. (2019) <arXiv:1906.00051>. DD-PCA can be used in covariance matrix estimation and global detection in multiple testing. This package implements DD-PCA using both convex approach and non-convex approach; Convex approach refers to solving a convex relaxation of the original problem using Alternating Direction Method of Multipliers (ADMM), while non-convex approach resorts to an iterative projection algorithm. This package also implements two global testing methods proposed in the reference.
Imports: RSpectra, Matrix, quantreg, MASS

Authors@R: c(person("Tracy", "Ke", email="zke@fas.harvard.edu", role=c("aut")),
person("Fan", "Yang", email="fyang1@uchicago.edu", role=c("aut", "cre")))
Description: Efficient procedures for fitting the DD-PCA (Ke et al., 2019, <arXiv:1906.00051>)  by decomposing a large covariance matrix into a low-rank matrix plus a diagonally dominant matrix. The implementation of DD-PCA includes the convex approach using the Alternating Direction Method of Multipliers (ADMM) and the non-convex approach using the iterative projection algorithm. Applications of DD-PCA to large covariance matrix estimation and global multiple testing are also included in this package.

Title: Analysis and Visualization of Droplet Digital PCR in R and on
person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"))
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for
analyzing duplex ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
Suggests: ggExtra (>= 0.3.0), graphics, grid (>= 3.2.2), gridExtra (>=
2.0.0), knitr (>= 1.7), rmarkdown, stats, testthat (>= 0.9.1),