This package provides a set of modular, pipeable functions to calculate PageRank scores from edge lists and redirect reports, common in SEO analysis. Functions handle URL cleaning, redirect resolution, edge deduplication, isolate handling, and PageRank computation using base R for data manipulation and igraph for core PageRank calculation.

Integration of two data sources referred to the same target population which share a number of variables. Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.

This package provides function for small area estimation at area level using averaging pseudo area level model for variables of interest. A dataset produced by data generation is also provided. This package estimates small areas at the village level and then aggregates them to the sub-district, region, and provincial levels.

Bayesian spatial models for survey data, such as Demographic and Health Survey (DHS), with spatial cluster location displacement adjustments. The package implements models for (1) continuous, (2) binary, (3) count and (4) spatially varying models for continuous outcomes. For more details see Bakar et al. (2026) <doi:10.1093/jrsssa/qnag068>.

Useful to visualize the Poissoneity (an independent Poisson statistical framework, where each RNA measurement for each cell comes from its own independent Poisson distribution) of Unique Molecular Identifier (UMI) based single cell RNA sequencing (scRNA-seq) data, and explore cell clustering based on model departure as a novel data representation.

Reveals how data quality silently degrades during geographic transformations while variable labels remain unchanged. Demonstrates that transformation error is agnostic to both the variable (population, income, etc.) and the tool ('R', Python', etc.). Provides a reproducible audit framework for quantifying the shift from observed to imputed data at each transformation hop.

This package provides tools for measuring similarity among documents and detecting passages which have been reused. Implements shingled n-gram, skip n-gram, and other tokenizers; similarity/dissimilarity functions; pairwise comparisons; minhash and locality sensitive hashing algorithms; and a version of the Smith-Waterman local alignment algorithm suitable for natural language.

Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.

This package provides an R interface to OpenFHE', the open-source C++ library for fully homomorphic encryption (Al Badawi and others, 2022) <https://eprint.iacr.org/2022/915>, which allows computation directly on encrypted data without access to the secret key. Supports the Brakerski-Fan-Vercauteren (BFV, 2012) <https://eprint.iacr.org/2012/144>, Brakerski-Gentry-Vaikuntanathan (BGV, 2014) <doi:10.1145/2633600>, and Cheon-Kim-Kim-Song (CKKS, 2017) <https://eprint.iacr.org/2016/421> schemes for arithmetic on encrypted numbers, together with the Ducas-Micciancio (FHEW, 2015) <https://eprint.iacr.org/2014/816> and Chillotti-Gama-Georgieva-Izabachene (TFHE, 2020) <https://eprint.iacr.org/2018/421> schemes for evaluating arbitrary functions on encrypted bits.

This is an extension of the regression-based causal mediation analysis first proposed by Valeri and VanderWeele (2013) <doi:10.1037/a0031034> and Valeri and VanderWeele (2015) <doi:10.1097/EDE.0000000000000253>). It supports including effect measure modification by covariates(treatment-covariate and mediator-covariate product terms in mediator and outcome regression models) as proposed by Li et al (2023) <doi:10.1097/EDE.0000000000001643>. It also accommodates the original SAS macro and PROC CAUSALMED procedure in SAS when there is no effect measure modification. Linear and logistic models are supported for the mediator model. Linear, logistic, loglinear, Poisson, negative binomial, Cox, and accelerated failure time (exponential and Weibull) models are supported for the outcome model.

This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.

This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.

Relx assembles releases for an Erlang/OTP release. Given a release specification and a list of directories in which to search for OTP applications it will generate a release output. That output depends heavily on what plugins available and what options are defined, but usually it is simply a well configured release directory.

This package provides a convenient way to access the LINCS Signatures available in the iLINCS database. These signatures include Consensus Gene Knockdown Signatures, Gene Overexpression signatures and Chemical Perturbagen Signatures. It also provides a way to enter your own transcriptomic signatures and identify concordant and discordant signatures in the LINCS database.

FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.

Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002).

Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.

This package provides customized print methods for SummarizedExperiment objects to enhance readability and usability within a tidy workflow. It offers consistent, tidyverse-aligned console displays, including alternative tibble abstractions for large genomic data to improve discoverability and interpretation. The package also includes unified, contextual messaging utilities intended for the tidyomics ecosystem.

Clinical trial design for subgroup selection in three-stage group sequential trial as described in Lai, Lavori and Liao (2014, <doi:10.1016/j.cct.2014.09.001>). Includes facilities for design, exploration and analysis of such trials. An implementation of the initial DEFUSE-3 trial is also provided as a vignette.

The functions defined in this program serve for implementing adaptive two-stage tests. Currently, four tests are included: Bauer and Koehne (1994), Lehmacher and Wassmer (1999), Vandemeulebroecke (2006), and the horizontal conditional error function. User-defined tests can also be implemented. Reference: Vandemeulebroecke, An investigation of two-stage tests, Statistica Sinica 2006.

This package provides an integrated data management solution for assets installed via the Biobricks.ai platform. Streamlines the process of loading and interacting with diverse datasets in a consistent manner. A list of bricks is available at <https://status.biobricks.ai>. Documentation for Biobricks.ai is available at <https://docs.biobricks.ai>.

BabyTime is an application for tracking infant and toddler care activities like sleeping, eating, etc. This package will take the outputted .zip files and parse it into a usable list object with cleaned data. It handles malformed and incomplete data gracefully and is designed to parse one directory at a time.

This package provides an R interface to the Evolution API <https://evoapicloud.com>, enabling sending and receiving WhatsApp messages directly from R'. Functions include sending text, media (image/video/document), audio, stickers, geographic locations, contacts, polls, interactive lists and button messages. Also includes number verification and structured CLI logging for debugging.