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A Future API for Parallel and Distributed Processing using 'batchtools'
Implementation of the Future API on top of the 'batchtools' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, not only on your local machine or ad-hoc cluster of machines, but also via high-performance compute ('HPC') job schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS', e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Analysis of Large Affymetrix Microarray Data Sets
A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Batch Computing with R
Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.
R Interface to the Pushbullet Messaging Service
An R interface to the Pushbullet messaging service which provides fast and efficient notifications (and file transfer) between computers, phones and tablets. An account has to be registered at the site http://www.pushbullet.com site to obtain a (free) API key.
Simple Memory Profiling for R
A simple and light-weight API for memory profiling of R expressions. The profiling is built on top of R's built-in memory profiler ('utils::Rprofmem()'), which records every memory allocation done by R (also native code).
Methods for Reading dChip Files
Functions for reading DCP and CDF.bin files generated by the dChip software.
Friendly R Startup Configuration
Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.
A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
A Future API for Parallel Processing using 'callr'
Implementation of the Future API on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession'), the 'callr' backend provided here can run more than 125 parallel R processes.
Copy-Number Analysis of Large Microarray Data Sets
Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.