MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames.

This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.

Package regexp implements regular expression search. The syntax of the regular expressions accepted is the same general syntax used by Perl, Python, and other languages. More precisely, it is the syntax accepted by RE2 and described at https://golang.org/s/re2syntax, except for \C.

This library enables path variables in networking routes when using Hunchenissr for Common Lisp. If a part of the path (between two slashes) starts with a question mark (?), that symbol (without question mark) will be bound to whatever value was in the same place in the URL (as a string).

This module is for reading record-oriented data in a delimited text file. The most common example have records separated by newlines and fields separated by commas or tabs, but this module aims to provide a consistent interface for handling sequential records in a file however they may be delimited.

This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005).

Linux driver for USB WiFi adapters that are based on the Realtek RTL8811CU, RTL8821CU, RTL8821CUH and RTL8731AU chipsets.

To work, in addition to installing the driver, you need to disable the conflicting rtw88 driver:

(operating-system
  ;; ...
  ;; Blacklist conflicting kernel modules.
  (kernel-arguments '("modprobe.blacklist=rtw88_8821cu"))
  (kernel-loadable-modules (list rtl8821cu-linux-module)))

The chemformula package and babel-russian settings both define macros named \ch. This package un-defines Babel's macro to prevent an error when both packages are loaded together. Optionally, it redefines the \cosh macro to print the hyperbolic cosine in Russian notation or defines a new macro \Ch for that purpose.

PowerMock is a framework that extends other mock libraries such as EasyMock with more powerful capabilities. PowerMock uses a custom classloader and bytecode manipulation to enable mocking of static methods, constructors, final classes and methods, private methods, removal of static initializers and more. By using a custom classloader no changes need to be done to the IDE or continuous integration servers which simplifies adoption.

The Resources Plugin handles the copying of project resources to the output directory. There are two different kinds of resources: main resources and test resources. The difference is that the main resources are the resources associated to the main source code while the test resources are associated to the test source code.

Thus, this allows the separation of resources for the main source code and its unit tests.

ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a fast pseudo-random number generator. It is suitable for applications where a significant amount of random data needs to be produced quickly, such as solving using the Monte Carlo method or for games. The results are uniformly distributed, unbiased, and unpredictable unless you know the seed.

This package provides a Perl interface to the ISAAC pseudo random number generator.

This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.

SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the citation function and see <https://doi.org/10.1371/journal.pcbi.1011324>.

The runtime is the executable part of every AppImage. It mounts the payload via FUSE and executes the entrypoint, allowing users to run applications in a portable manner without the need for installation. This runtime ensures that the AppImage can access its bundled libraries and resources seamlessly, providing a consistent environment across different Linux distributions. In the absence of FUSE, the AppImage can still be started using the --appimage-extract-and-run flag.

transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).

Documentation at https://melpa.org/#/org-re-reveal-ref

Affymetrix ragene20 annotation data (chip ragene20stprobeset) assembled using data from public repositories.

Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories.

Affymetrix ragene11 annotation data (chip ragene11stprobeset) assembled using data from public repositories.

Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories.

Rspec-expectations provides a simple API to express expected outcomes of a code example.

Rspec-expectations provides a simple API to express expected outcomes of a code example.

This wrapper around rclone makes any destination supported by rclone usable with git-annex.