A shiny app for browsing and annotating scRNAseq clusters.
This package is still experimental!
SingleCellExperiment
objectsRequired R packages for the app:
BiocManager::install(c( "Seurat", "shiny","shinydashboard","shinycssloaders",
"DT", "data.table", "ggplot2", "cowplot", "AnnotationDbi", "GO.db" ) )
Package clustree
is also required:
devtools::install_github("lazappi/clustree", dependencies = TRUE)
In addition, preparing the cluster annotation will require the appropriate org.Xx.eg.db
for your species, e.g. org.Hs.eg.db
.
I tried to make it backward-compatible with Seurat v2, but right now it's only tested with V3. To install Seurat V3:
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/3.0')
To install ClustView
:
devtools::install_github("plger/clustView")
Assuming a seurat object named se
, first get all markers for each cluster/resolution. For example, in v3 (assuming the default prefix after integration):
library(clustView)
# get all computed resolutions:
cn <- names(seurat@meta.data)
resolutions <- as.numeric(gsub("integrated_snn_res.","",cn[grep("^integrated_snn_res",cn)],fixed=T))
# get markers for each cluster/resolution:
markers <- list()
for(r in resolutions){
markers[[as.character(r)]] <- FindAllMarkers(
object = se,
only.pos = FALSE,
min.pct = 0.25,
resolution = r,
logfc.threshold = 0.5,
test.use = "wilcox",
max.cells.per.ident = 300 )
}
se <- prepSeuratForClustView( se,
markerslist=markers,
species="Hs",
ontologies=c("BP", "CC") )
Assuming a seurat object named se
:
clustView(se)
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