SPICEY
Calculates cell type specificity from single cell data
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SPICEY")Details
| Maintainer | Georgina Fuentes-Páez <georgina.fuentes@upf.edu> |
| Author | Georgina Fuentes-Páez [aut, cre] (ORCID: <https://orcid.org/0009-0003-9417-7148>), Nacho Molina [aut], Mireia Ramos-Rodriguez [aut], Lorenzo Pasquali [aut], Ministerio de Ciencia e Innovación Spain [fnd] (program: FPI Fellowship) |
| License | Artistic-2.0 |
| URL | https://georginafp.github.io/SPICEY |
| Bug Reports | https://github.com/georginafp/SPICEY/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, DifferentialPeakCalling, Epigenetics, GeneExpression, GeneRegulation, GeneTarget, SingleCell, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/SPICEY/ |
Citation
From within R, enter citation("SPICEY"):
Georgina Fuentes-Páez, Nacho Molina, Mireia Ramos-Rodriguez, Lorenzo Pasquali. SPICEY: Calculates cell type specificity from single cell data. doi:10.18129/B9.bioc.SPICEY, R package version 1.3.0, https://bioconductor.org/packages/SPICEY.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SPICEY_1.3.0.tar.gz |
| Windows binary (x86_64) | SPICEY_1.3.0.zip |
| macOS binary (arm64) | SPICEY_1.3.0.tgz |
| macOS binary (x86_64) | SPICEY_1.3.0.tgz |
Dependencies
Depends: R (>= 4.5.0), utils, stats, grDevices
Imports: GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors, ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot
Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>= 3.0.0)