SPICEY

Bioconductor release status

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devel
release

The goal of SPICEY is to provide a user-friendly pipeline for quantifying and visualizing tissue specificity specificity

Installation

You can install the latest release of SPICEY the github repository:

devtools::install_github("georginafp/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").

# Load needed libraries
library(SPICEY)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
library(dplyr)
library(GenomicRanges)
library(cicero)

# Compute GETSI 
results <- run_spicey(rna = rna, gene_id = "gene_id")

# Compute RETSI
results <- run_spicey(atac=atac)

# Compute GETSI + RETSI
results <- run_spicey(atac=atac, rna=rna, gene_id = "gene_id")

# Compute GETSI + RETSI and link RE to target genes through nearest gene method
result <- run_spicey(
  atac = atac, 
  rna = rna, 
  gene_id = "gene_id",
  annot_method = "nearest", 
  txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
  annot_dbi = org.Hs.eg.db,
  link_spicey_measures = TRUE
)

# Compute GETSI + RETSI and link RE to target genes through coaccessibility method
result <- run_spicey(
  atac = atac, 
  rna = rna, 
  gene_id = "gene_id",
  annot_method = "coaccessibility",
  links = coaccess_links,
  txdb = TxDb.Hsapiens.UCSC.hg38.knownGene
)

# Compute GETSI + RETSI and link RE to target genes through coaccessibility method
# and link both SPICEY measures
result <- run_spicey(
  atac = atac, 
  rna = rna, 
  gene_id = "gene_id",
  link_spicey_measures = TRUE,
  annot_method = "coaccessibility",
  links = coaccess_links,
  txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
)

Code of Conduct

Please note that the SPICEY project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.