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).

Analysis of Parent-Specific DNA Copy Numbers

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Fit a Principal Curve in Arbitrary Dimension

Fitting a principal curve to a data matrix in arbitrary dimensions. Hastie and Stuetzle (1989) .

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 < https://www.pushbullet.com> site to obtain a (free) API key.

Easily Install and Load the 'Futureverse'

The 'Futureverse' is a set of packages for parallel and distributed process with the 'future' package at its core, cf. Bengtsson (2021) . This package is designed to make it easy to install and load multiple 'Futureverse' packages in a single step. This package is intended for end-users, interactive use, and R scripts. Packages must not list it as a dependency - instead, explicitly declare each 'Futureverse' package as a dependency as needed.

Sequence Globally Unique Identifier (SEGUID) Checksums

Implementation of the original Sequence Globally Unique Identifier (SEGUID) algorithm [Babnigg and Giometti (2006) ] and SEGUID v2 (< https://www.seguid.org>), which extends SEGUID v1 with support for linear, circular, single- and double-stranded biological sequences, e.g. DNA, RNA, and proteins.

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.)

Methods for Accessing Huge Amounts of Data [deprecated]

DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)