scHOT

DOI: 10.18129/B9.bioc.scHOT    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see scHOT.

single-cell higher order testing

Bioconductor version: 3.14

Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.

Author: Shila Ghazanfar [aut, cre], Yingxin Lin [aut]

Maintainer: Shila Ghazanfar <shazanfar at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("scHOT")

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("scHOT")

 

HTML	R Script	Getting started: scHOT
PDF		Reference Manual

Details

biocViews	GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	S4Vectors(>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics
LinkingTo
Suggests	knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir
SystemRequirements
Enhances
URL
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	scHOT_1.6.0.tar.gz
Windows Binary	scHOT_1.6.0.zip
macOS 10.13 (High Sierra)	scHOT_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scHOT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scHOT
Package Short Url	https://bioconductor.org/packages/scHOT/
Package Downloads Report	Download Stats