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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.

Versions across snapshots

VersionRepositoryFileSize
1.0.0 rolling linux/jammy R-4.5 scquantum_1.0.0.tar.gz 35.3 KiB
1.0.0 rolling linux/noble R-4.5 scquantum_1.0.0.tar.gz 35.4 KiB
1.0.0 rolling source/ R- scquantum_1.0.0.tar.gz 10.7 KiB
1.0.0 latest linux/jammy R-4.5 scquantum_1.0.0.tar.gz 35.3 KiB
1.0.0 latest linux/noble R-4.5 scquantum_1.0.0.tar.gz 35.4 KiB
1.0.0 latest source/ R- scquantum_1.0.0.tar.gz 10.7 KiB
1.0.0 2026-04-26 source/ R- scquantum_1.0.0.tar.gz 10.7 KiB
1.0.0 2026-04-23 source/ R- scquantum_1.0.0.tar.gz 10.7 KiB
1.0.0 2026-04-09 windows/windows R-4.5 scquantum_1.0.0.zip 41.8 KiB
1.0.0 2025-04-20 source/ R- scquantum_1.0.0.tar.gz 10.7 KiB

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