RedNotebook is a modern desktop journal. It lets you format, tag and search your entries. You can also add pictures, links and customizable templates, spell check your notes, and export to plain text, HTML, Latex or PDF.

This library allows reading and writing RPM packages. It is used by the fpm tool. It is written in pure Ruby because librpm is not available on all systems and requires many dependencies.

As everyone knows, the most complex codes were composed of a mass of different kinds of parentheses (typically: lisp). This plugin will help you read these codes by showing different levels of parentheses in different colors.

Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).

Solving a system of linear equations is one of the most fundamental computational problems for many fields of mathematical studies, such as regression problems from statistics or numerical partial differential equations. This package provides basic stationary iterative solvers such as Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. Nonstationary, also known as Krylov subspace methods are also provided. Sparse matrix computation is also supported in that solving large and sparse linear systems can be manageable using the Matrix package along with RcppArmadillo.

This package provides a simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level.

Rope is a refactoring library for Python. It facilitates the renaming, moving and extracting of attributes, functions, modules, fields and parameters in Python source code. These refactorings can also be applied to occurrences in strings and comments.

rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.

This package provides tools to produce a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot.

Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

This package provides fundamental physical constants (quantity, value, uncertainty, unit) for SI and non-SI units, plus unit conversions based on the data from NIST, USA.

This package provides a syntax highlighter for R code based on the results of the R parser. It supports rendering in HTML and LaTeX markup. It includes a custom Sweave driver performing syntax highlighting of R code chunks.

Radix trees, or tries, are key-value data structures optimized for efficient lookups, similar in purpose to hash tables. This package provides an implementation of radix trees for use in R programming and in developing packages with Rcpp.

This package provides functions for the truncated normal distribution with mean equal to mean and standard deviation equal to sd. It includes density, distribution, quantile, and expected value functions, as well as a random generation function.

Spring is a Ruby on Rails application preloader. It speeds up development by keeping your application running in the background so the application does need to boot it every time you run a test, rake task or migration.

This package provides a multitude of tools for comparative genomics, focused on large-scale analyses of biological data. SynExtend includes tools for working with syntenic data, clustering massive network structures, and estimating functional relationships among genes.

This package provides a dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessibility for new Bioconductor users is hopefully increased.

This package contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.

This package provides generic functions for interacting with the AnVIL system. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.

This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for quantitative language comparison (QLC).

Cyclomatic complexity is a software metric, used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code. This package provides tools to compute this metric.

The tidyverse is a set of packages that work in harmony because they share common data representations and API design. This package is designed to make it easy to install and load multiple tidyverse packages in a single step.

React is an OCaml module for functional reactive programming (FRP). It provides support to program with time varying values: declarative events and signals. React doesn't define any primitive event or signal, it lets the client choose the concrete timeline.

The file renaming utilities (renameutils for short) are a set of programs designed to make renaming of files faster and less cumbersome. The file renaming utilities consists of five programs: qmv, qcp, imv, icp, and deurlname.