scHOT
This is the released version of scHOT; for the devel version, see scHOT.
single-cell higher order testing
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | scHOT_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | scHOT_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | scHOT_1.24.0.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 |