Provides a novel functionality to correct the center in segmentation data obtained from copy number calling tools such as CopyNumber450k and ChAMP. CopyNumber450kCancer implements the maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct the baseline in cancer samples. The main advantages for CopyNumber450kCancer are: fast auto-correction (few seconds per sample), high accuracy rate, in-sample correction, no input parameters needed, low computer resources required, and adaptable to 450k-similar technologies.

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CopyNumber450kCancer classification

CopyNumber450kCancer specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
CopyNumber450kCancer version 1.0.4
Requirements:
R (≥ 3.1.0)

Publications

  • (Marzouka et al., 2015) CopyNumber450kCancer: Baseline Correction for Accurate Copy Number Calling from the 450k Methylation Array. Bioinformatics.
    PMID: 26553913

CopyNumber450kCancer support

Documentation

Maintainer

Credits

Institution(s)

Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden

Funding source(s)

The Swedish Cancer Society [CAN2010/592]; the Swedish Research Council for Science and Technology [90559401]; the Swedish Foundation for Strategic Research [RBc08-008]

Link to literature

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