This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

This package offers a flexible statistical simulator for scRNA-seq data. It can generate data that captures gene correlation. Additionally, it allows for varying the number of cells and sequencing depth.

This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e., static .html files). It currently supports linked brushing and filtering.

Density discontinuity testing (a.k.a. manipulation testing) is commonly employed in regression discontinuity designs and other program evaluation settings to detect perfect self-selection (manipulation) around a cutoff where treatment/policy assignment changes. This package implements manipulation testing procedures using the local polynomial density estimators: rddensity() to construct test statistics and p-values given a prespecified cutoff, rdbwdensity() to perform data-driven bandwidth selection, and rdplotdensity() to construct density plots.

Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal RPC protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our JSS paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of Protocol Buffers library is required; currently version 3.3.0 from 2017 is the stated minimum.

Presentation-ready results tables for epidemiologists in an automated, reproducible fashion. The user provides the final analytical dataset and specifies the design of the table, with rows and/or columns defined by exposure(s), effect modifier(s), and estimands as desired, allowing to show descriptors and inferential estimates in one table -- bridging the rift between epidemiologists and their data, one table at a time. See Rothman (2017) <doi:10.1007/s10654-017-0314-3>.

rust-base is a zero-dependency library for working with base62 encoding with Rust. base62 is typically used for URL shorteners. It can optionally use io traits from the standard library.

Static code compilation of a shiny app given an R function (into ui.R and server.R files or into a shiny app object). See examples at <https://github.com/alekrutkowski/autoshiny>.

Interact with the Attentional Control Data Collection (ACDC). Connect to the database via connect_to_db(), set filter arguments via add_argument() and query the database via query_db().

Generation of multiple binary and continuous non-normal variables simultaneously given the marginal characteristics and association structure based on the methodology proposed by Demirtas et al. (2012) <DOI:10.1002/sim.5362>.

This package contains a variety of methods to generate typical causal inference estimates using Bayesian Additive Regression Trees (BART) as the underlying regression model (Hill (2012) <doi:10.1198/jcgs.2010.08162>).

Wrangle country data more effectively and quickly. This package contains functions to easily identify and convert country names, download country information, merge country data from different sources, and make quick world maps.

Computes the maximum likelihood estimator, the smoothed maximum likelihood estimator and pointwise bootstrap confidence intervals for the distribution function under current status data. Groeneboom and Hendrickx (2017) <doi:10.1214/17-EJS1345>.

Evaluate arbitrary function calls using workers on HPC schedulers in single line of code. All processing is done on the network without accessing the file system. Remote schedulers are supported via SSH.

Given response y, continuous predictor x, and covariate matrix, the relationship between E(y) and x is estimated with a shape constrained regression spline. Function outputs fits and various types of inference.

Apply styles to tag elements directly and with the .style pronoun. Using the pronoun, styles are created within the context of a tag element. Change borders, backgrounds, text, margins, layouts, and more.

An implementation of methods for causal discovery in a structural causal model where the conditional distribution of the target node is described by a generalized linear model conditional on its causal parents.

Color palettes inspired by the works of Mexican painters and muralists. The package includes functions that return vectors of colors and also functions to use color and fill scales in ggplot2 visualizations.

This package provides functions for generating variants of curves: restricted cubic spline, periodic restricted cubic spline, periodic cubic spline. Periodic splines can be used to model data that has periodic nature / seasonality.

An interactive document on the topic of basic probability using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://analyticmodels.shinyapps.io/BayesShiny/>.

Send push notifications to mobile devices or the desktop using Pushover <https://pushover.net>. These notifications can display things such as results, job status, plots, or any other text or numeric data.

Adds a Super Learner ensemble model method (using the SuperLearner package) to the mice package. Laqueur, H. S., Shev, A. B., Kagawa, R. M. C. (2021) <doi:10.1093/aje/kwab271>.

An open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments.See full documentation at <https://avi-kenny.github.io/SimEngine/>.

This package provides functions to take samples of data, sample size estimation and getting useful estimators such as total, mean, proportion about its population using simple random, stratified, systematic and cluster sampling.