Predicts the presence of signal peptides in eukaryotic protein using hidden semi-Markov models. The implemented algorithm can be accessed from both the command line and GUI.

This package provides functions to speed up the exploratory analysis of simple datasets using dplyr'. Functions are provided to do the common tasks of calculating confidence intervals.

Split a dataframe, tibble, or data.table into training and test sets. Return either a list, an index, or directly assign training and test sets into memory.

This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively.

Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.

This package provides a rolling version of the Latent Dirichlet Allocation, see Rieger et al. (2021) <doi:10.18653/v1/2021.findings-emnlp.201>. By a sequential approach, it enables the construction of LDA-based time series of topics that are consistent with previous states of LDA models. After an initial modeling, updates can be computed efficiently, allowing for real-time monitoring and detection of events or structural breaks.

SyncroSim is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). rsyncrosim provides an interface to SyncroSim'. Simulation models can be added to SyncroSim in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. rsyncrosim requires SyncroSim 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).

Studies of resilience in older adults employ a single-arm design where everyone experiences the stressor. The simplistic approach of regressing change versus baseline yields biased estimates due to regression-to-the-mean. This package provides a method to correct the bias. It also allows covariates to be included. The method implemented in the package is described in Varadhan, R., Zhu, J., and Bandeen-Roche, K (2023), Biostatistics (To appear).

This package provides a collection of tools to import and structure the (currently) single-season event, game-log, roster, and schedule data available from <https://www.retrosheet.org>. In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse. This package does the parsing on those files, returning the requested data in the most practical R structure to use for sabermetric or other analyses.

This package provides a small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode.

This package provides a collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.

The ammeter gem makes it easy to write specs for Rails generators. An existing user is rspec-rails, which uses ammeter to spec its own generators.

Promise is a Ruby implementation of the Promises/A+ specification. It provides 100% mutation coverage, tested on MRI 1.9, 2.0, 2.1, 2.2, Rubinius, and JRuby.

This package provides tools for sampling from the PolyaGamma distribution based on Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Useful for logistic regression.

This package provides functions for demographic analysis including lifetable calculations; Lee-Carter modelling; functional data analysis of mortality rates, fertility rates, net migration numbers; and stochastic population forecasting.

This package contains additional miscellaneous steps for the recipes package. These steps are useful, but doesn't have a good home in other recipes packages or its extensions.

This package provides tools for general properties including price, quantity, elasticity, convexity, marginal revenue and manifold of various economics demand systems including Linear, Translog, CES, LES and CREMR.

This package provides functions for fitting data to a quiescent growth model, i.e. a growth process that involves members of the population who stop dividing or propagating.

Genotype plus genotype-by-environment (GGE) biplots rendered using ggplot2'. Provides a command line interface to all of the functionality contained within the archived package GGEBiplotGUI'.

This package provides functions for inference of ploidy from (Genotyping-by-sequencing) GBS data, including a function to infer allelic ratios and allelic proportions in a Bayesian framework.

This package contains functions to construct high-dimensional orthogonal maximin distance designs in two, four, eight, and sixteen levels from rotating the Kronecker product of sub-Hadamard matrices.

Tool for generating quality reports from cruncher outputs (and calculating series scores). The latest version of the cruncher can be downloaded here: <https://github.com/jdemetra/jwsacruncher/releases>.

This package provides extensions to the leaflet package to customize legends with images, text styling, orientation, sizing, and symbology and functions to create symbols to plot on maps.

This package contains a sample of the 2005 Grade 8 Mathematics data from the National Assessment of Educational Progress (NAEP). This data set is called the NAEP Primer.