scquantum

Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing

CRAN Package

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.


Documentation


Team


Insights

Last 30 days

Last 365 days

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.

Data provided by CRAN


Binaries


Dependencies

  • Suggests1 package