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]
All associated links for this package
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
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
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
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

CompoundEvents  
Statistical Modeling of Compound Events
Tools for extracting occurrences, assessing potential driving factors, predicting occurrences, and q ...
Download / Learn more Package Citations See dependency  
MatrixEQTL  
Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for associat ...
Download / Learn more Package Citations See dependency  
stagePop  
Modelling the Population Dynamics of a Stage-Structured Species in Continuous Time
Provides facilities to implement and run population models of stage-structured species... ...
Download / Learn more Package Citations See dependency  
ismev  
An Introduction to Statistical Modeling of Extreme Values
Functions to support the computations carried out in `An Introduction to Statistical Modeling of Ex ...
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  
gclus  
Clustering Graphics
Orders panels in scatterplot matrices and parallel coordinate displays by some merit index. Package ...
Download / Learn more Package Citations See dependency  

22,114

R Packages

188,080

Dependencies

55,244

Author Associations

22,115

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net. Contact Us / Suggestions / Concerns