# SPICEY <img src="man/figures/SPICEY_LOGO_LIGHT.svg" width="200px" height="200px" align="right" style="padding-left:10px;background-color:white;"/>
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## Bioconductor release status
| Branch | R CMD check | Last updated |
|:------------------------:|:------------------------:|:-------------------:|
| [*devel*](http://bioconductor.org/packages/devel/bioc/html/SPICEY.html) | [](http://bioconductor.org/checkResults/devel/bioc-LATEST/SPICEY) |  |
| [*release*](http://bioconductor.org/packages/release/bioc/html/SPICEY.html) | [](http://bioconductor.org/checkResults/release/bioc-LATEST/SPICEY) |  |
The goal of SPICEY is to provide a user-friendly pipeline for quantifying and visualizing tissue specificity specificity
## Installation
Install the latest release of SPICEY from Bioconductor:
```{r install, eval=FALSE, echo=TRUE}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SPICEY")
```
Now you can load the package using `library(SPICEY)`.
## Basic usage
For detailed instructions on how to use SPICEY, please see the vignette once the package is installed using: `vignette("SPICEY")`.
``` r
library(dplyr)
library(GenomicRanges)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
library(SPICEY)
# Annotate peaks to genes with coaccessibility
peaks <- unique(unlist(atac)[,c("region_id")])
annotation_coacc <- annotate_with_coaccessibility(
peaks = peaks,
txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
links_df = cicero_links,
annot_dbi = org.Hs.eg.db,
protein_coding_only = TRUE,
verbose = TRUE,
add_tss_annotation = FALSE,
upstream = 2000,
downstream = 2000
)
# Calculate SPICEY measures and link them with coaccessibility
spicey_coacc <- SPICEY(
rna = rna,
atac = atac,
annotation = annotation_coacc
)
# Plot results
spicey_heatmap(spicey_coacc$linked,
spicey_measure = "SPICEY",
combined_score = TRUE)
```
<img src="man/figures/README-SPICEY_combined_plot.png" width="50%" />
## Code of Conduct
Please note that the SPICEY project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
