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Description

Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing.

Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) <doi:10.1002/0471667196.ess2129.pub2>, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) <doi:10.1080/10618600.2012.681238>, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.

scquantum

Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) \doi{10.1002/0471667196.ess2129.pub2}, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) \doi{10.1080/10618600.2012.681238}, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.

Metadata

Version

1.0.0

License

Unknown

Platforms (75)

    Darwin
    FreeBSD
    Genode
    GHCJS
    Linux
    MMIXware
    NetBSD
    none
    OpenBSD
    Redox
    Solaris
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