scquantum
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.
- Version1.0.0
- R versionunknown
- LicenseGPL-2
- LicenseGPL-3
- Needs compilation?Yes
- Last release03/23/2022
Documentation
Team
Alexander Davis
Taylor Arnold
Show author detailsRolesCopyright holderRyan Tibshirani
Show author detailsRolesCopyright holderVeeranjaneyulu Sadhanala
Show author detailsRolesCopyright holder
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