This package provides a project infrastructure with a focus on manuscript creation. Creates a project folder with a single command, containing subdirectories for specific components, templates for manuscripts, and so on.

This package provides a coding assistant using Perplexity's Large Language Models <https://www.perplexity.ai/> API. A set of functions and RStudio add-ins that aim to help R developers.

Compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data <https://github.com/fumi-github/scPloidy>.

Latent space models for multivariate networks (multiplex) estimated via MCMC algorithm. See D Angelo et al. (2018) <arXiv:1803.07166> and D Angelo et al. (2018) <arXiv:1807.03874>.

This package provides tools to perform some descriptive data analysis for assets. Manage the portfolio and capital of assets. It also downloads and organizes data from the Tehran Stock Exchange (TSE).

Performing the hypothesis tests for the two sample problem based on order statistics and power comparisons. Calculate the test statistic, density, distribution function, quantile function, random number generation and others.

This package provides a suite of easy to use functions for collecting social media data and generating networks for analysis. Supports Mastodon, YouTube, Reddit and Web 1.0 data sources.

This package provides formatting linting to roxygen2 tags. Linters report roxygen2 tags that do not conform to a standard style. These linters can be a helpful check for building more consistent documentation and to provide reminders about best practices or checks for typos. Default linting suites are provided for common style guides such as the one followed by the tidyverse', though custom linters can be registered by other packages or be custom-tailored to a specific package.

The routine twosample_test() in this package runs the two sample test using various test statistic. The p values are found via permutation or large sample theory. The routine twosample_power() allows the calculation of the power in various cases, and plot_power() draws the corresponding power graphs. The routine run.studies allows a user to quickly study the power of a new method and how it compares to some of the standard ones.

This package provides a custom implementation of the apriori algorithm and binomial tests to identify combinations of features (genes, variants etc) significantly enriched for simultaneous mutations/events from sparse Boolean input, see Vijay Kumar Pounraja, Santhosh Girirajan (2021). Version 1.1 includes a minor adjustment to the number of combinations to be considered for multiple testing correction. This updated version is more conservative in its approach and hence more selective. <doi:10.1101/2021.10.01.462832>.

An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>, a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD). Due to the possible portability issues CRAN version no longer supports OpenMP, but you can install OpenMP-supported version from GitHub: <https://github.com/helske/Rlibeemd/>.

This package contains data which are used by functions of the abc package which implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.

This package provides tools for the maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); it includes inference and basic methods.

This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both hcubature and pcubature routines in addition to a vector interface.

Reply is a lightweight, extensible REPL for Perl. It is plugin-based (see Reply::Plugin), and through plugins supports many advanced features such as coloring and pretty printing, readline support, and pluggable commands.

Namae (名前) is a parser for human names. It recognizes personal names of various cultural backgrounds and tries to split them into their component parts (e.g., given and family names, honorifics etc.).

Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University.

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

API for using episensr', Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. See <https://cran.r-project.org/package=episensr>.

Handy frameworks, such as error handling and log generation, for batch scripts. Use case: in scripts running in remote servers, set error handling mechanism for downloading and uploading and record operation log.

An interactive document on the topic of classification tree analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://kartikeyab.shinyapps.io/CTShiny/>.

Client for the Open Citations Corpus (<http://opencitations.net/>). Includes a set of functions for getting one identifier type from another, as well as getting references and citations for a given identifier.

This package provides tools for connecting to CHILDES', an open repository for transcripts of parent-child interaction. For more information on the underlying data, see <https://langcog.github.io/childes-db-website/>.

Calculates permutation tests that can be powerful for comparing two groups with some positive but many zero responses (see Follmann, Fay, and Proschan <DOI:10.1111/j.1541-0420.2008.01131.x>).