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single-cell higher order testing

Bioconductor version: Release (3.19)

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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Getting started: scHOT HTML R Script
Reference Manual PDF


biocViews GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.16.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
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Suggests knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir
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Package Archives

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

Source Package scHOT_1.16.0.tar.gz
Windows Binary
macOS Binary (x86_64) scHOT_1.16.0.tgz
macOS Binary (arm64) scHOT_1.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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