CRAN/E | scquantum

scquantum

Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing

Installation

About

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.

Key Metrics

Version 1.0.0
Published 2022-03-23 929 days ago
Needs compilation? yes
License GPL-2
License GPL-3
CRAN checks scquantum results

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Maintainer

Maintainer

Alexander Davis

Authors

Alexander Davis

aut / cre

Taylor Arnold

cph

(Author of segmentation function)

Veeranjaneyulu Sadhanala

cph

(Author of segmentation function)

Ryan Tibshirani

cph

(Author of segmentation function)

Material

README
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Suggests

testthat ≥ 3.0.0