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scShapes

This is the development version of scShapes; for the stable release version, see scShapes.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("scShapes")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
The vignette for running scShapes HTML R Script
Reference Manual PDF

Details

biocViews GeneExpression, MultipleComparison, RNASeq, SingleCell, Software
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils
System Requirements
URL https://github.com/Malindrie/scShapes
Bug Reports https://github.com/Malindrie/scShapes/issues
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Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

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

Source Package scShapes_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64) scShapes_1.9.0.tgz
macOS Binary (arm64)
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/
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