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calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

The CalMaTe method calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.

Version: 0.13.0
Depends: R (≥ 3.2.1), R.utils (≥ 2.11.0), aroma.core (≥ 3.2.2)
Imports: utils, MASS, R.methodsS3 (≥ 1.8.1), R.oo (≥ 1.24.0), matrixStats (≥ 0.61.0), R.filesets (≥ 2.14.0)
Suggests: DNAcopy
Published: 2022-03-08
DOI: 10.32614/CRAN.package.calmate
Author: Maria Ortiz [aut, ctb], Ander Aramburu [ctb], Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut, ctb], Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson <henrikb at braju.com>
BugReports: https://github.com/HenrikBengtsson/calmate/issues
License: LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]
URL: https://github.com/HenrikBengtsson/calmate/
NeedsCompilation: no
Citation: calmate citation info
Materials: README NEWS
CRAN checks: calmate results

Documentation:

Reference manual: calmate.pdf

Downloads:

Package source: calmate_0.13.0.tar.gz
Windows binaries: r-devel: calmate_0.13.0.zip, r-release: calmate_0.13.0.zip, r-oldrel: calmate_0.13.0.zip
macOS binaries: r-release (arm64): calmate_0.13.0.tgz, r-oldrel (arm64): calmate_0.13.0.tgz, r-release (x86_64): calmate_0.13.0.tgz, r-oldrel (x86_64): calmate_0.13.0.tgz
Old sources: calmate archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.