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README.md
In scquantum: Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing
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.
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scquantum documentation built on March 23, 2022, 9:07 a.m.
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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.
Try the scquantum package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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