SPICEY
This is the development version of SPICEY; to use it, please install the devel version of Bioconductor.
Calculates cell type specificity from single cell data
Bioconductor version: Development (3.22)
SPICEY (SPecificity Index for Coding and Epigenetic activitY) is an R package designed to quantify cell-type specificity in single-cell transcriptomic and epigenomic data, particularly scRNA-seq and scATAC-seq. It introduces two complementary indices: the Gene Expression Tissue Specificity Index (GETSI) and the Regulatory Element Tissue Specificity Index (RETSI), both based on entropy to provide continuous, interpretable measures of specificity. By integrating gene expression and chromatin accessibility, SPICEY enables standardized analysis of cell-type-specific regulatory programs across diverse tissues and conditions.
Author: Georgina Fuentes-Páez [aut, cre]
, Nacho Molina [aut], Mireia Ramos-Rodriguez [aut], Lorenzo Pasquali [aut], Ministerio de Ciencia e Innovación Spain [fnd] (program: FPI Fellowship)
Maintainer: Georgina Fuentes-Páez <georgina.fuentes at upf.edu>
citation("SPICEY")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SPICEY")
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("SPICEY")| Measuring tissue specificity from single cell data with SPICEY | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, DifferentialPeakCalling, Epigenetics, GeneExpression, GeneRegulation, GeneTarget, SingleCell, Software, Transcription, Transcriptomics |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), utils, stats, grDevices |
| Imports | GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors, ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot |
| System Requirements | |
| URL | https://georginafp.github.io/SPICEY |
| Bug Reports | https://github.com/georginafp/SPICEY/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) |
| 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 | SPICEY_0.99.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | SPICEY_0.99.3.tgz |
| macOS Binary (arm64) | SPICEY_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SPICEY |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SPICEY |
| Bioc Package Browser | https://code.bioconductor.org/browse/SPICEY/ |
| Package Short Url | https://bioconductor.org/packages/SPICEY/ |
| Package Downloads Report | Download Stats |