The package uses collectbox to define variants of common box related macros which read the content as real box and not as macro argument. This enables the use of verbatim or other special material as part of this content. The provided macros have the same names as the original versions but start with an upper-case letter instead. The long-form macros, like \Makebox, can also be used as environments, but not the short-form macros, like \Mbox. However, normally the long form uses the short form anyway when no optional arguments are used.

systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.

Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately).

This package defines a BigMatrix ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a file-system-based permissions system. Utilities are provided for using BigMatrix-derived classes as assayData matrices within the Biobase package's eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a BigMatrixFactor class, a file-backed matrix with factor properties.

The komacv-rg bundle provides packages that aid in creating CVs based on the komacv class and creating related documents, such as cover letters and cover sheets for job applications.

Concretely, the bundle consists of three packages: komacv-addons, komacv-lco, and komacv-multilang. komacv-addons is a small collection of add-ons and fixes for the komacv class; komacv-lco enables the use of letter class options from scrlttr2 also in komacv-based and other non-scrlttr2-based documents; komacv-multilang enables the provisioning of CVs in multiple languages and the selection of a language via Babel or Polyglossia.

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

git-remote-gcrypt is a Git remote helper to push and pull from repositories encrypted with GnuPG. It works with the standard Git transports, including repository hosting services like GitLab.

Remote helper programs are invoked by Git to handle network transport. This helper handles gcrypt: URLs that access a remote repository encrypted with GPG, using our custom format.

Supported locations are local, rsync:// and sftp://, where the repository is stored as a set of files, or instead any Git URL where gcrypt will store the same representation in a Git repository, bridged over arbitrary Git transport.

The aim is to provide confidential, authenticated Git storage and collaboration using typical untrusted file hosts or services.

Package graphicx provides a useful keyword viewport which allows to show just a part of an image. However, one needs to put there the actual coordinates of the viewport window. Sometimes it is useful to have relative coordinates as fractions of natural size. For example, one may want to print a large image on a spread, putting a half on a verso page, and another half on the next recto page. For this one would need a viewport occupying exactly one half of the file's bounding box, whatever the actual width of the image may be. This package adds a new keyword rviewport to the graphicx package specifying relative viewport for graphics inclusion: a window defined by the given fractions of the natural width and height of the image.

systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.

This package provides a plugin for the RuboCop code style enforcing & linting tool.

Support utilities for RSpec gems.

Documentation at https://melpa.org/#/rails-routes

Documentation at https://melpa.org/#/realgud-rdb2

RequestStore gives you per-request global storage.

Platform Design Info for Affymetrix Clariom_S_Rat.

This package provides Rake tasks to generate and check a manifest file.

Microarray gene expression data from the study of Vawter et al., 2004.

Affymetrix rta10 annotation data (chip rta10probeset) assembled using data from public repositories.

Platform Design Info for Affymetrix RaGene-2_1-st.

Platform Design Info for Affymetrix RaGene-2_0-st.

Rake-compiler provides a framework for building and packaging native C and Java extensions in Ruby.

RTG-MATH provides a selection of the math routines most commonly needed for making realtime graphics in Lisp.

babel selfContained runtime