The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

Nyxt is a keyboard-oriented, extensible web-browser designed for power users. The application has familiar Emacs and VI key-bindings and is fully configurable and extensible in Common Lisp.

Some basic features of MUMPS are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: PORD, METIS, SCOTCH.

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.

R-escape streamlines gene set enrichment analysis for single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.

This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.

This package provides a ggplot2 extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.

Inspired by the the futile.logger R package and logging Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.

The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.

This package lets you manage configuration values across multiple environments (e.g. development, test, production). It reads values using a function that determines the current environment and returns the appropriate value.

This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.

Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

The CSV library provides a complete interface to CSV files and data. It offers tools to enable you to read and write to and from Strings or IO objects, as needed.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

This package extends the ggplot2 plotting system which implements a grammar of graphics. ggtree is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

This package conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.

This package provides an infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). It also provides C implementations of the association mining algorithms Apriori and Eclat.

This package provides key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.

RESTinio is a header-only C++14 library that gives you an embedded HTTP/Websocket server. It is based on standalone version of ASIO and targeted primarily for asynchronous processing of HTTP-requests.