Allspice: RNA-Seq Profile Classifier

We developed a lightweight machine learning tool for RNA profiling of acute lymphoblastic leukemia (ALL), however, it can be used for any problem where multiple classes need to be identified from multi-dimensional data. The methodology is described in Makinen V-P, Rehn J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia, medRxiv, <doi:10.1101/2022.02.17.22270919>. The classifier contains optimized mean profiles of the classes (centroids) as observed in the training data, and new samples are matched to these centroids using the shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL patients are included, but users can train the models with their own data as well. The output includes both numerical and visual presentations of the classification results. Samples with mixed features from multiple classes or atypical values are also identified.

Version: 1.0.4
Imports: methods
Suggests: knitr, rmarkdown
Published: 2022-04-13
Author: Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Citation: Allspice citation info
CRAN checks: Allspice results

Documentation:

Reference manual: Allspice.pdf
Vignettes: intro

Downloads:

Package source: Allspice_1.0.4.tar.gz
Windows binaries: r-devel: Allspice_1.0.4.zip, r-release: Allspice_1.0.4.zip, r-oldrel: Allspice_1.0.4.zip
macOS binaries: r-release (arm64): Allspice_1.0.4.tgz, r-oldrel (arm64): Allspice_1.0.4.tgz, r-release (x86_64): Allspice_1.0.4.tgz, r-oldrel (x86_64): Allspice_1.0.4.tgz
Old sources: Allspice archive

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