scShapes

DOI: 10.18129/B9.bioc.scShapes  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scShapes.

A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data

Bioconductor version: 3.16

We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.

Author: Malindrie Dharmaratne [cre, aut]

Maintainer: Malindrie Dharmaratne <malindrie at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scShapes")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scShapes")

 

HTML	R Script	The vignette for running scShapes
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, MultipleComparison, RNASeq, SingleCell, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils
LinkingTo
Suggests	knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/Malindrie/scShapes
BugReports	https://github.com/Malindrie/scShapes/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scShapes_1.4.0.tar.gz
Windows Binary	scShapes_1.4.0.zip
macOS Binary (x86_64)	scShapes_1.4.0.tgz
macOS Binary (arm64)	scShapes_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scShapes
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scShapes
Bioc Package Browser	https://code.bioconductor.org/browse/scShapes/
Package Short Url	https://bioconductor.org/packages/scShapes/
Package Downloads Report	Download Stats