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scquantum  

Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing
View on CRAN: Click here


Download and install scquantum package within the R console
Install from CRAN:
install.packages("scquantum")

Install from Github:
library("remotes")
install_github("cran/scquantum")

Install by package version:
library("remotes")
install_version("scquantum", "1.0.0")



Attach the package and use:
library("scquantum")
Maintained by
Alexander Davis
[Scholar Profile | Author Map]
First Published: 2022-03-23
Latest Update: 2022-03-23
Description:
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) , 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) , using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.
How to cite:
Alexander Davis (2022). scquantum: Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing. R package version 1.0.0, https://cran.r-project.org/web/packages/scquantum. Accessed 29 Mar. 2025.
Previous versions and publish date:
No previous versions
Other packages that cited scquantum R package
View scquantum citation profile
Other R packages that scquantum depends, imports, suggests or enhances
Complete documentation for scquantum
Functions, R codes and Examples using the scquantum R package
Some associated functions: internals . ploidy.inference . 
Some associated R codes: internals.R . ploidy_inference.R .  Full scquantum package functions and examples
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