scHOT
This is thereleased version of scHOT; for the devel version, seescHOT.
single-cell higher order testing
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("scHOT")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("scHOT")| Getting started: scHOT | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression,RNASeq,Sequencing,SingleCell,Software,Transcriptomics |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 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 | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | scHOT_1.22.0.tar.gz |
| Windows Binary (x86_64) | scHOT_1.22.0.zip |
| macOS Binary (x86_64) | scHOT_1.22.0.tgz |
| macOS Binary (arm64) | scHOT_1.22.0.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 |