Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples.

This is a package for significance analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

Remake is an enhanced version of GNU Make that adds improved error reporting, better tracing, profiling, and a debugger.

Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.

This package provides a dependency management toolkit for R. Using renv, you can create and manage project-local R libraries, save the state of these libraries to a lockfile, and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.

This package provides functions for testing affine hypotheses on the regression coefficient vector in regression models with autocorrelated errors.

This package provides convenience functions for data preparation and modeling often used in analytical customer relationship management (aCRM).

This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.

This package provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.

This package provides tools for measuring inequality, concentration, and poverty measures. It provides both empirical and theoretical Lorenz curves.

This package provides tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).

This package converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination. All functions can use exact infinite-precision rational arithmetic.

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.

This package allows you to render vector-based SVG images into high-quality custom-size bitmap arrays using the librsvg2 library. The resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In addition, the package can convert images directly to various formats such as PDF or PostScript.

This package lets you perform unsupervised clustering of amplicon sequencing data in microbiome studies with the Dirichlet-tree Multinomial Mixtures.

This package adds 3D perspective plotting of points, paths, and line, 3D perspective axes, 3D perspective annotations, and wireframe plots.

This package provides a more comfortable interface to work with R data or source files in a key-value fashion.

This package provides useful tools to pry back the covers of R and understand the language at a deeper level.

This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

This is a framework for construction and analysis of 2D Monte-Carlo simulations. In addition, this package includes various distributions.

This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools.

The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods.

This package provides R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.