This package is an implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. This package single-cell analysis via expression recovery (SAVER) implements an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.

This package provides other packages with access to the internal R serialization code. Access to this code is provided at the C function level by using the registration of native function mechanism. Client packages simply include a single header file RApiSerializeAPI.h provided by this package.

This is a data only package providing the algorithmic complexity of short strings, computed using the coding theorem method. For a given set of symbols in a string, all possible or a large number of random samples of Turing machines with a given number of states (e.g., 5) and number of symbols corresponding to the number of symbols in the strings were simulated until they reached a halting state or failed to end. This package contains data on 4.5 million strings from length 1 to 12 simulated on Turing machines with 2, 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the distribution of the halting states.

This package provides means to run simulations for adaptive seamless designs with and without early outcomes for treatment selection and subpopulation type designs.

This package provides functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).

This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key) encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and bignum math methods for manually performing crypto calculations on large multibyte integers.

This package provides a custom CSS/HTML or GIF/image file for the loading screen in R Shiny. It also can use the marquee to have a custom text loading screen.

This package lets you generate random or human readable and pronounceable identifiers.

This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.

This package provides a generalized estimating equations solver for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. It can also handle clustered categorical responses.

The function missForest in this package is used to impute missing values, particularly in the case of mixed-type data. It uses a random forest trained on the observed values of a data matrix to predict the missing values. It can be used to impute continuous and/or categorical data, including complex interactions and non-linear relations. It yields an OOB imputation error estimate without the need of a test set or elaborate cross- validation. It can be run in parallel to save computation time.

This package provides code analysis tools for R to check R code for possible problems.

Parametric time warping aligns patterns. It aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS error and WCC. Both warping of peak profiles and of peak lists are supported.

This package implements easy-to-use functions to generate 2-7 sets Venn plot in publication quality. ggVennDiagram plot Venn using well-defined geometry dataset and ggplot2. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package venn. We provide internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in three components: set edges, set labels, and regions. From version 1.0, it is possible to customize these components as you demand in ordinary ggplot2 grammar.

This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models.

This package provides an interface to Amazon Web Services management and governance services, including CloudWatch application and infrastructure monitoring, Auto Scaling for automatically scaling resources, and more.

This package provides type-stable rolling window functions over any R data type. Cumulative and expanding windows are also supported. For more advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.

For tree ensembles such as random forests, regularized random forests and gradient boosted trees, this package provides functions for: extracting, measuring and pruning rules; selecting a compact rule set; summarizing rules into a learner; calculating frequent variable interactions; formatting rules in latex code. Reference: Interpreting tree ensembles with inTrees (Houtao Deng, 2019, <doi:10.1007/s41060-018-0144-8>).

This package provides MathJax and macros to enable its use within Rd files for rendering equations in the HTML help files.

This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.

This package provides an R interface to the libgit2 library, which is a pure C implementation of the Git core methods.

This package generates area-proportional Euler diagrams using numerical optimization. An Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented. Diagrams may be fit with ellipses and circles via a wide range of inputs and can be visualized in numerous ways.

This package provides functions to export graphics drawn with package grid to SVG format. Extra functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.

The Gaussian hypergeometric function for complex numbers.