SplineDV
This is thereleased version of SplineDV; for the devel version, seeSplineDV.
Differential Variability (DV) analysis for single-cell RNA sequencing data. (e.g. Identify Differentially Variable Genes across two experimental conditions)
Bioconductor version: Release (3.22)
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: 0000-0002-1904-9862, James Cai [aut] ORCID: 0000-0002-8081-6725
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")BiocManager::install("SplineDV")For older versions of R, please refer to the appropriateBioconductor 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 | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | SplineDV_1.2.0.tar.gz |
| Windows Binary (x86_64) | SplineDV_1.2.0.zip |
| macOS Binary (x86_64) | SplineDV_1.2.0.tgz |
| macOS Binary (arm64) | SplineDV_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SplineDV |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SplineDV |
| Bioc Package Browser | https://code.bioconductor.org/browse/SplineDV/ |
| Package Short Url | https://bioconductor.org/packages/SplineDV/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.22 | Source Archive |