Other packages > Find by keyword >

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 22 Apr. 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
Downloads during the last 30 days
03/2303/2403/2503/2603/2703/2803/2903/3003/3104/0104/0204/0304/0404/0504/0604/0704/0804/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/20Downloads for scquantum02468101214161820TrendBars

Today's Hot Picks in Authors and Packages

GWPR.light  
Geographically Weighted Panel Regression
Geographically weighted panel regression is grounded in a branch of spatial statistics. Using geogra ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
phylosamp  
Sample Size Calculations for Molecular and Phylogenetic Studies
Implements novel tools for estimating sample sizes needed for phylogenetic studies, including studi ...
Download / Learn more Package Citations See dependency  
ino  
Initialization of Numerical Optimization
Analysis of the initialization for numerical optimization of real-valued functions, including likel ...
Download / Learn more Package Citations See dependency  
optimStrat  
Choosing the Sample Strategy
Intended to assist in the choice of the sampling strategy to implement in a survey. ...
Download / Learn more Package Citations See dependency  
Qest  
Quantile-Based Estimator
Quantile-based estimators (Q-estimators) can be used to fit any parametric distribution, using its q ...
Download / Learn more Package Citations See dependency  

24,098

R Packages

207,311

Dependencies

65,069

Author Associations

24,099

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA