This package allows clinicians to predict the rate and severity of future acute exacerbation in Chronic Obstructive Pulmonary Disease (COPD) patients, based on the clinical prediction model published in Adibi et al. (2019) doi:10.1101/651901.

MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.

Omixer - an Bioconductor package for multivariate and reproducible sample randomization, which ensures optimal sample distribution across batches with well-documented methods. It outputs lab-friendly sample layouts, reducing the risk of sample mixups when manually pipetting randomized samples.

redumper is a low-level byte perfect CD disc dumper. It supports incremental dumps, advanced SCSI/C2 repair, intelligent audio CD offset detection, among other features. redumper is also a general purpose DVD/HD-DVD/Blu-ray disc dumper.

Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Additional examples, documentations, and details on the method are available at https://github.com/kharchenkolab/hahmmr/.

Lefser is an implementation in R of the popular "LDA Effect Size" (LEfSe) method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.

This package provides a data.table backend for dplyr. The goal of dtplyr is to allow you to write dplyr code that is automatically translated to the equivalent, but usually much faster, data.table code.

This package provides procedures to answer the following questions: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have?

This package is a collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a tidyverse workflow.

Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide replacement functions for the ACM licensed akima::interp and tripack::tri.mesh functions.

This package provides a functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.

This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

This package allows for the estimation of a wide variety of advanced multivariate statistical models. It consists of a library of functions and optimizers that allow you to quickly and flexibly define an SEM model and estimate parameters given observed data.

Tidyft is an extension of data.table. It uses modifification by reference whenever possible. This toolkit is designed for big data analysis in high-performance desktop or laptop computers. The syntax of the package is similar or identical to tidyverse.

This package provides tools and functions for parsing, rendering and operating on semantic version strings. Semantic versioning is a simple set of rules and requirements that dictate how version numbers are assigned and incremented as outlined at http://semver.org.

This package includes HTML functions and methods to write in an HTML file. Thus, making HTML reports is easy. It includes a function that allows redirection on the fly, which appears to be very useful for teaching purposes, as the student can keep a copy of the produced output to keep all that they did during the course. The package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for Sweave parses HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).

This package provides a framework for the analysis and exploration of single-cell chromatin data. The Signac package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.

This package provides type-stable rolling window functions over any R data type. Cumulative and expanding windows are also supported. For more advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.

This package provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications.

This package contains the resample and windowfilter command line utilities. The resample command allows changing the sampling rate of a sound file, while the windowfilter command allows designing Finite Impulse Response (FIR) filters using the so-called window method.