matter

Scientific computing for out-of-memory signals and images

Toolbox for out-of-memory scientific computing and data visualization, providing memory-efficient file-based data structures for dense and sparse vectors, matrices, and arrays with applications to nonuniformly sampled signals and images.

Description

The Matter package provides flexible data structures for out-of-memory computing on dense and sparse arrays, with specialized features designed specifically for computing on nonuniform signals such as mass spectra and other spectral data, as well as hyperspectral images.

Matter 2 has been updated to provide a more robust C++ backend to out-of-memory matter objects, along with a completely new implementation of sparse arrays. Tools for signal processing, dimension reduction, and data visualization are also provided.

User Installation

Bioconductor Release

Matter can be installed via the BiocManager package.

This is the recommended installation method.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("matter")

The same function can be used to update Matter and other Bioconductor packages.

Once installed, Matter can be loaded with library():

library(matter)

Github Release

Matter can also be installed via the remotes package.

if (!require("remotes", quietly = TRUE))
    install.packages("remotes")

remotes::install_github("kuwisdelu/matter", ref=remotes::github_release())

Previous releases can be installed by specifying the exact version.

remotes::install_github("kuwisdelu/[email protected]")

Developer Installation

Bioconductor Devel

The Bioconductor development version of matter can also be installed via the BiocManager package.

BiocManager::install("matter", version="devel")

This version is unstable and should not be used for critical work. However, it is typically more stable than Github devel.

This version should typically pass R CMD check without errors.

Github Devel

The most cutting edge version of Matter can be installed from Github via the remotes package.

if (!require("remotes", quietly = TRUE))
    install.packages("remotes")

remotes::install_github("kuwisdelu/matter")

This version is unstable and only recommended for developers. It should not be used for critical work.