scTHI
This is the development version of scTHI; for the stable release version, see scTHI.
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Bioconductor version: Development (3.24)
scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.
Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre]
Maintainer: Michele Ceccarelli <m.ceccarelli at gmail.com>
citation("scTHI")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scTHI")
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("scTHI")| Using scTHI | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | SingleCell, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.0) |
| Imports | BiocParallel, Rtsne, grDevices, graphics, stats |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/miccec/scTHI/issues |
See More
| Suggests | scTHI.data, knitr, rmarkdown, BiocStyle |
| 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 | scTHI_1.25.0.tar.gz |
| Windows Binary (x86_64) | scTHI_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | scTHI_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | scTHI_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scTHI |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scTHI |
| Bioc Package Browser | https://code.bioconductor.org/browse/scTHI/ |
| Package Short Url | https://bioconductor.org/packages/scTHI/ |
| Package Downloads Report | Download Stats |