The HiTC package was developed to explore high-throughput "C" data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.

This package provides functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.

This package lets you construct paths to your project's files. Use the here function as a drop-in replacement for file.path, it will always locate the files relative to your project root.

Reaver performs a brute force attack against an access point's Wi-Fi Protected Setup (WPS) PIN. Once the PIN is found, the WPA passphrase can be recovered and the AP's wireless settings can be reconfigured.

This package helps with the analysis of array CGH data by detecting of the breakpoints in the genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

This package contains linear and nonlinear regression methods based on partial least squares and penalization techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.

This package contains:

• facilities for working with grouped data: do something to data stratified by some variables.

• implementations of least-squares means, general linear contrasts, and

• miscellaneous other utilities.

Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.

REAPER is a digital audio production application offering multitrack audio and MIDI recording, editing, processing, mixing and mastering toolset. It supports a vast range of hardware, digital formats and plugins, and can be comprehensively extended, scripted and modified.

This package provides a framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. It imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.

GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. The library includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

This package provides a system for organizing column names in data. It is aimed at supporting a prefix-based and suffix-based column naming scheme. It extends dplyr functionality to add ordering by function and more explicit renaming.

Assigning probability scores to protein interactions captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein-protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data.

This package provides linear models based on Theil-Sen single median and Siegel repeated medians. They are very robust (29 or 50 percent breakdown point, respectively), and if no outliers are present, the estimators are very similar to OLS.

This package provides bindings to the OSQP solver. The OSQP solver is a numerical optimization package or solving convex quadratic programs written in C and based on the alternating direction method of multipliers. See <arXiv:1711.08013> for details.

The ability to tune models is important. tune contains functions and classes to be used in conjunction with other tidymodels packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.

rocFFT is a software library for computing fast Fourier transforms (FFTs) written in the HIP programming language. It's part of AMD's software ecosystem based on ROCm. The rocFFT library can be used with AMD and NVIDIA GPUs.

rsgain (really simple gain) is a ReplayGain 2.0 command line utility. rsgain applies loudness metadata tags to your files, while leaving the audio stream untouched. A ReplayGain-compatible player will dynamically adjust the volume of your tagged files during playback.

The zlog package offers functions to transform laboratory measurements into standardised z or z(log)-values. Therefore the lower and upper reference limits are needed. If these are not known they could be estimated from a given sample.

Originally inspired by Unity IMGUI (immediate mode GUI API).

Designed as an auxiliary module for raylib to create simple GUI interfaces using raylib graphic style (simple colors, plain rectangular shapes, wide borders...) but it can be adapted to other engines/frameworks.

Rspamd is an advanced spam filtering system that allows evaluation of messages by a number of rules including regular expressions, statistical analysis and custom services such as URL black lists. Each message is analysed by Rspamd and given a spam score.

rocHPL is a benchmark based on the HPL benchmark application, implemented on top of AMD's Radeon Open Compute ROCm Platform, runtime, and toolchains. rocHPL is created using the HIP programming language and optimized for AMD's latest discrete GPUs.

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.