rst.linker automatically replaces text by a reStructuredText external reference or timestamps. It's primary purpose is to augment the changelog, but it can be used for other documents, too.

This package defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.

This module provides line editing support via the Readline library for GNU Guile. Use the (ice-9 readline) module and call its activate-readline procedure to enable it.

ProgressBar is a simple library for displaying progress bars. The maximum value is configurable, and additional information can be displayed like the percentage completion, estimated time remaining, elapsed time and rate.

lib::relative module proposes a more straightforward method than adding a path to @INC: take a path relative to the current file, absolutize it, and add it to @INC.

jaro_winkler is an implementation of Jaro-Winkler distance algorithm. It is written as a C extension and will fallback to a pure Ruby implementation on platforms where this is unsupported.

This package provides tools for detecting drug-protein interactions and estimating IC50 values from chemoproteomics data. Implements semi-parametric isotonic regression, bootstrapping, and curve fitting to evaluate compound effects on protein abundance.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430A\_2\_probe\_tab.

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

dvc-render is a library for rendering data stored in DVC plots format into different output formats, like Vega. It can also generate HTML and MarkDown reports containing multiple plots.

This program is derived from comint-mode and provides the following features:

• TAB completion same as Node.js REPL

• file name completion in string

• incremental history search

This library lets elisp authors easily define an idiomatic command to reformat the current buffer using a command-line program, together with an optional minor mode which can apply this command automatically on save.

This package provides a class for typesetting scripts containing both lyrics and prose, in the style used by the student revues (revy) at the Faculties of Science at the University of Copenhagen (uchp).

This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.

RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.

This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

This is a comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. It provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

This package provides a set of predicates and assertions for checking the types of variables. This is mainly for use by other package developers who want to include run-time testing features in their own packages.

rotate-text allows you rotate to commonly interchanged text with a single keystroke. For example, you can toggle between "frame-width" and "frame-height", between "public", "protected" and "private" and between "variable1", "variable2" through "variableN".

Spectroscope is a Behavior-Driven Development (BDD) framework built on RubyTest, designed to emulate RSpec in most respects. It is assertion framework independent so any number of assertion systems can be used, such as Assay or AE.

EventMachine implements a single-threaded engine for arbitrary network communications. EventMachine wraps all interactions with sockets, allowing programs to concentrate on the implementation of network protocols. It can be used to create both network servers and clients.

This package speeds up the derfinder package when using multiple cores. It is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.

This is a package for estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.