This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.

This package provides a package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.

Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors (see Teschendorff AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).

This package implements both real-valued branches of the Lambert-W function (Corless et al, 1996) <doi:10.1007/BF02124750> without the need for installing the entire GSL.

Provide nonparametric methods for mean regression model, modal regression and conditional density estimation in the presence/absence of measurement error. Bandwidth selection is also provided for each method.

This package proposes a new file format named gson for storing gene set and related information, and provides read, write and other utilities to process this file format.

This package provides an integrated set of functions for the analysis of multivariate normal datasets with missing values, including implementation of the EM algorithm, data augmentation, and multiple imputation.

r-kmer is an R package for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.

This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.

This package provides the Rakarrack effects as LV2 plugins. The ports are done such that hopefully when Rakarrack gets an active maintainer these will get merged into the original project.

This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.

Rdfind is a command line tool that finds duplicate files based on their content instead of their file names. It is useful for compressing backup directories or just finding duplicate files.

This package provides a Perl interface (Perl::Rename) as well as a command-line utility (rename) that can rename multiple files at once based on a Perl regular expression.

This package provides an interface to Amazon Web Services, including storage, database, and compute services, such as Simple Storage Service (S3), DynamoDB NoSQL database, and Lambda functions-as-a-service.

UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.

St implements a simple and lightweight terminal emulator. It implements 256 colors, most VT10X escape sequences, utf8, X11 copy/paste, antialiased fonts (using fontconfig), fallback fonts, resizing, and line drawing.

This package lets you fit beta regression and zero-or-one inflated beta regression and obtain Bayesian inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.

Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R.

This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors.

This package provides functions to handle basic input output. These functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.