scHOT
single-cell higher order testing
Bioconductor version: Release (3.20)
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("scHOT")):
Installation
To install this package, start R (version "4.4") 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")| Getting started: scHOT | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir |
| 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 | scHOT_1.18.0.tar.gz |
| Windows Binary (x86_64) | scHOT_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | scHOT_1.18.0.tgz |
| macOS Binary (arm64) | scHOT_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scHOT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scHOT |
| Bioc Package Browser | https://code.bioconductor.org/browse/scHOT/ |
| Package Short Url | https://bioconductor.org/packages/scHOT/ |
| Package Downloads Report | Download Stats |