DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.

Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.

This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.

OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.

Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.

The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

latex2exp parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.

This package provides functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.

This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies.

Merlin is a STROBE-based transcript construction for zero-knowledge proofs. It automates the Fiat-Shamir transform, so that by using Merlin, non-interactive protocols can be implemented as if they were interactive.

Merlin is a STROBE-based transcript construction for zero-knowledge proofs. It automates the Fiat-Shamir transform, so that by using Merlin, non-interactive protocols can be implemented as if they were interactive.

Erubis is a fast implementation of embedded Ruby (eRuby) with several features such as multi-language support, auto escaping, auto trimming spaces around <% %>, a changeable embedded pattern, and Ruby on Rails support.

Sequel provides thread safety, connection pooling and a concise DSL for constructing SQL queries and table schemas. It includes a comprehensive ORM layer for mapping records to Ruby objects and handling associated records.

This package provides functions to query (filter or transform), pivot (convert from array-of-objects to object-of-arrays, for easy import as R data frame), search, patch (edit), and validate (against JSON Schema') JSON and NDJSON strings, files, or URLs. Query and pivot support JSONpointer', JSONpath or JMESpath expressions. The implementation uses the jsoncons <https://danielaparker.github.io/jsoncons/> header-only library; the library is easily linked to other packages for direct access to C++ functionality not implemented here.

Parse R code in a given directory for R packages and attempt to install them from CRAN or GitHub. Optionally use a dependencies file for tighter control over which package versions to install.

An interactive document on the topic of binary logistic regression analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://analyticmodels.shinyapps.io/BinaryLogisticRegressionModelling/>.

Compares two dataframes which have the same column structure to show the rows that have changed. Also gives a git style diff format to quickly see what has changed in addition to summary statistics.

This package provides a minimum set of functions to perform compositional data analysis using the log-ratio approach introduced by John Aitchison (1982). Main functions have been implemented in c++ for better performance.

Implementation of a probabilistic method for biclustering adapted to overdispersed count data. It is a Gamma-Poisson Latent Block Model. It also implements two selection criteria in order to select the number of biclusters.

Bindings to qpdf': qpdf (<https://qpdf.sourceforge.io/>) is a an open-source PDF rendering library that allows to conduct content-preserving transformations of PDF files such as split, combine, and compress PDF files.

Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.

Create groups of ggplot2 layers that can be easily migrated from one plot to another, reducing redundant code and improving the ability to format many plots that draw from the same source ggpacket layers.

Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.