Detect and remove chimeras from your amplicon sequence analysis using reference-based or de novo approaches. The rchime package implements the VSEARCH algorithms described in Rognes et al. (2016) <doi:10.7717/peerj.2584>. VSEARCH builds on the work of Edgar,R.C. et al. (2011) <doi:10.1093/bioinformatics/btr381>.

Fully DBI'-compliant interface to Greenplum <https://greenplum.org/>, an open-source parallel database. This is an extension of the RPostgres package <https://github.com/r-dbi/RPostgres>.

This package provides a collection of tools for measuring the similarity of text messages and tracing the flow of messages over time and across media.

Rank-based, asymptotic distribution-free change-point detection for modern (high-dimensional, non-Euclidean) data, based on the graph-induced ranking scheme of Zhou and Chen (2025) <doi:10.1109/TIT.2025.3575858>. Given a rank matrix built from a pairwise similarity, the method scans for a single change-point or a changed interval using three statistics (weighted WR', max-type MR', and generalized TR') and returns analytic distribution-free p-value approximations (with an optional skewness correction) as well as optional permutation p-values.

This package provides a client for the API of OpenDota. OpenDota is a web service which is provide DOTA2 real time data. Data is collected through the Steam WebAPI. With ROpenDota you can easily grab the latest DOTA2 statistics in R programming such as latest match on official international competition, analyzing your or enemy performance to learn their strategies,etc. Please see <https://github.com/rosdyana/ROpenDota> for more information.

This package provides functions to manipulate rational functions, including basic arithmetic operators, derivatives, and integrals with EXPLICIT forms.

Use trend filtering, a type of regularized nonparametric regression, to estimate the instantaneous reproduction number, also called Rt. This value roughly says how many new infections will result from each new infection today. Values larger than 1 indicate that an epidemic is growing while those less than 1 indicate decline. For more details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024) <doi:10.1371/journal.pcbi.1012324>.

This package provides methods for calculating diversity indices on numerical matrices, based on information theory, following Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039> and Rocchini et al. (2021) <doi:10.1101/2021.01.23.427872>.

Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of ruminate is to create a shiny interface to make these tools more broadly available while creating reproducible results.

Dump source code, documentation and vignettes of an R package into a single file. Supports installed packages, tar.gz archives, and package source directories. If the package is not installed, only its source is automatically downloaded from CRAN for processing. The output is a single plain text file or a character vector, which is useful to ingest complete package documentation and source into a large language model (LLM) or pass it further to other tools, such as ragnar <https://github.com/tidyverse/ragnar> to create a Retrieval-Augmented Generation (RAG) workflow.

Implementation of the RPC-JSON API for Bitcoin and utility functions for address creation and content analysis of the blockchain.

Focused on (but not exclusive to) data sets hosted on PhysioNet (<https://physionet.org>), ricu provides utilities for download, setup and access of intensive care unit (ICU) data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented.

For a given suit, if you add up the number of cards that you hold, plus the number that has been played so far, you can easily determine the number that remains in the combined hands of your three opponents. You can also determine the ("special") card of highest rank of the remaining cards for that suit. At some point, you notice that a certain opponent discards that special card. What can you infer about his holding in that suit? A series of simulation studies are reported here that allows a quantitative inference based on the conditional probability, given that the opponent has the special card. The same procedure is also used for the conditional probability, given that the opponent does not have the special card.

Wrapper for Datamuse API to find rhyming and other associated words. This includes words of similar meaning, spelling, or other related words. Learn more about the Datamuse API here <https://www.datamuse.com/api/>.

This package provides functionality to interact with the FieldClimate API <https://api.fieldclimate.com/v2/docs/>.

SEA performs simultaneous feature-set testing for (gen)omics data. It tests the unified null hypothesis and controls the family-wise error rate for all possible pathways. The unified null hypothesis is defined as: "The proportion of true features in the set is less than or equal to a threshold." Family-wise error rate control is provided through use of closed testing with Simes test. There are some practical functions to play around with the pathways of interest.

BaseX <https://basex.org> is a XML database engine and a compliant XQuery 3.1 processor with full support of W3C Update Facility'. This package is a full client-implementation of the client/server protocol for BaseX and provides functionalities to create, manipulate and query on XML-data.

This package provides a full-featured RethinkDB <https://rethinkdb.com/> client for R; allows users to store JSON-serialised data in a robust, distributed no-SQL system, use rich queries and react to data changes in real-time.

This package contains functions to interface with variables and variable details sheets, including recoding variables and converting them to PMML.

An optimized method for identifying mutually exclusive genomic events. Its main contribution is a statistical analysis based on the Poisson-Binomial distribution that takes into account that some samples are more mutated than others. See [Canisius, Sander, John WM Martens, and Lodewyk FA Wessels. (2016) "A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>]. The mutations matrices are sparse matrices. The method developed takes advantage of the advantages of this type of matrix to save time and computing resources.

This package contains various tools to estimate, analyze, and visualize Response Item Networks. ResIN dummy-codes ordered and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.

Wraps dozens of REDCap API endpoints into a standardized R6 object. Research Electronic Data Capture ('REDCap') is a survey and database web application software maintained by Vanderbilt University. It has a robust application programming interface (API) utilized by several R packages. REDCapSync uses redcapAPI and REDCapR behind-the-scenes to retrieve all metadata, data, and log details for a project. To minimize unnecessary server calls, the interim REDCap log is analyzed and used to only update necessary records. Furthermore, the user can define custom datasets that save to a directory. Those datasets continue to refresh when projects are synced. Having a secure, standardized, API-efficient, project-agnostic R object for REDCap projects, streamlines downstream use in scripts, functions, and shiny applications.

An implementation of the Heroicons icon library for shiny applications and other R web-based projects. You can search, render, and customize icons without CSS or JavaScript dependencies.

Recursive partitioning methods to build classification trees for ordinal responses within the CART framework. Trees are grown using the Generalized Gini impurity function, where the misclassification costs are given by the absolute or squared differences in scores assigned to the categories of the response. Pruning is based on the total misclassification rate or on the total misclassification cost.