Ranch aims to provide everything you need to accept TCP connections with a small code base and low latency while being easy to use directly as an application or to embed into your own.

This package provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

This package offers functionality for taking methtuple or Bismark outputs to calculate ASM scores and compute DAMEs regions. It also offers nice visualization of methyl-circle plots.

This package provides enhanced message functions (cat() / message() / warning() / error()) using wrappers around sprintf(). It also provides multiple assertion functions (e.g. to check class, length, values, files, arguments, etc.).

This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

The lpSolveAPI package provides an R interface to lp_solve, a MILP, solver with support for pure linear, (mixed) integer/binary, semi-continuous and SOS models.

This package calls the Jupyter script nbconvert to create vignettes from notebooks. Those notebooks (.ipynb files) are files containing rich text, code, and its output. Code cells can be edited and evaluated interactively.

This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution).

This package is a Ruby parser library for Gemtext (hypertext format which is intended to serve as the native response format of the Gemini file transfer protocol) and produces a document object of various nodes.

This package efficiently obtains count vectors from indexed bam files. It counts the number of nucleotide sequence reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

This package is a collection of several algorithms to obtain archetypoids with small and large databases and with both classical multivariate data and functional data (univariate and multivariate). Some of these algorithms also detect anomalies (outliers).

The mapping gem maps model objects based on their class to a given output model. It is useful for versioning external interfaces (e.g. JSON APIs) or processing structured data from one format to another.

Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.

This r-rbenchmark package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.

Timecop provides "time travel" and "time freezing" capabilities, making it easier to test time-dependent code. It provides a unified method to mock Time.now, Date.today, and DateTime.now in a single call.

This package provides a backend for the selecting functions of the tidyverse. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other tidyverse interfaces for selection.

This package provides tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.

This package provides rpcsvc protocol.x files and headers that are not included with the libtirpc package. Additionally it contains rpcgen, which is used to produce header files and sources from the protocol files.

By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.