SplineDV
This is the development version of SplineDV; to use it, please install the devel version of Bioconductor.
Differential Variability (DV) analysis for single-cell RNA sequencing data. (e.g. Identify Differentially Variable Genes across two experimental conditions)
Bioconductor version: Development (3.21)
A spline based scRNA-seq method for identifying differentially variable (DV) genes across two experimental conditions. Spline-DV constructs a 3D spline from 3 key gene statistics: mean expression, coefficient of variance, and dropout rate. This is done for both conditions. The 3D spline provides the “expected” behavior of genes in each condition. The distance of the observed mean, CV and dropout rate of each gene from the expected 3D spline is used to measure variability. As the final step, the spline-DV method compares the variabilities of each condition to identify differentially variable (DV) genes.
Author: Shreyan Gupta [aut, cre] (ORCID:
Maintainer: Shreyan Gupta <xenon8778 at tamu.edu>
citation("SplineDV")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SplineDV")
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("SplineDV")| Introduction to Spline-DV | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, FeatureExtraction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 0.99.11 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | GPL-2 |
| Depends | R (>= 3.5.0) |
| Imports | plotly, dplyr, scuttle, methods, Biobase, BiocGenerics, S4Vectors, sparseMatrixStats, SingleCellExperiment, SummarizedExperiment, Matrix (>= 1.6.4), utils |
| System Requirements | |
| URL | https://github.com/Xenon8778/SplineDV |
| Bug Reports | https://github.com/Xenon8778/SplineDV/issues |
See More
| Suggests | knitr, DelayedMatrixStats, rmarkdown, BiocStyle, ggplot2, ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SplineDV_0.99.11.tar.gz |
| Windows Binary (x86_64) | SplineDV_0.99.11.zip |
| macOS Binary (x86_64) | SplineDV_0.99.11.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SplineDV |
| Source Repository (Developer Access) | git clone [email protected]:packages/SplineDV |
| Bioc Package Browser | https://code.bioconductor.org/browse/SplineDV/ |
| Package Short Url | https://bioconductor.org/packages/SplineDV/ |
| Package Downloads Report | Download Stats |