scHOT

DOI: 10.18129/B9.bioc.scHOT    

single-cell higher order testing

Bioconductor version: Release (3.11)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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, 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_1.0.0.tar.gz
Windows Binary scHOT_1.0.0.zip
macOS 10.13 (High Sierra) scHOT_1.0.0.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
Old Source Packages for BioC 3.11 Source Archive

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