iSEEid

The goal of iSEEid is to use iSEE to identify cells

Installation

Get the latest stable R release from CRAN.
Then, install iSEEid from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("iSEEid")

And the development version from GitHub with:

BiocManager::install("iSEE/iSEEid")

Example

We use the Allen Brain Atlas dataset from scRNAseq as a running example, pre-processed in a summary manner just for showing most functionality.

library("iSEEid")
library("iSEE")
library("scRNAseq")
library("scater")
library("scrapper")

sce <- ReprocessedAllenData(assays = "tophat_counts")
sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
sce <- runPCA(sce, ncomponents = 4)
sce <- runTSNE(sce)

colData(sce)["cell_type"] <- "unassigned"

sce # this is the SummarizedExperiment object you use to store your data

iSEE(sce, initial = list(
  ReducedDimensionPlot(
    PanelWidth = 6L
  ),
  SampleIdentificationCenter(
    ColumnSelectionSource = "ReducedDimensionPlot1",
    PanelWidth = 6L
  )
))

Disclaimer

The large language model claude.ai (Sonnet 4.6) has been used in conversational mode to enable the output format switch in the panel, to comply with the remainder of iSEE’s architecture. Code suggestions have been revised and validated before committing them.

Code of Conduct

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