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A toolkit for performing KNN-based statistics for flow and mass cytometry data

Bioconductor version: Release (3.19)

This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold.

Author: Tyler J Burns

Maintainer: Tyler J Burns <burns.tyler at>

Citation (from within R, enter citation("Sconify")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Data Quality HTML R Script
Final Post-Processing Steps for Scone HTML R Script
Finding Ideal K HTML R Script
General Scone Analysis HTML R Script
How to process FCS files for downstream use in R HTML R Script
Reference Manual PDF


biocViews FlowCytometry, ImmunoOncology, MultipleComparison, SingleCell, Software, Visualization
Version 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5)
Imports tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr
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Suggests knitr, rmarkdown, testthat
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Follow Installation instructions to use this package in your R session.

Source Package Sconify_1.24.0.tar.gz
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macOS Binary (x86_64) Sconify_1.24.0.tgz
macOS Binary (arm64) Sconify_1.24.0.tgz
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Source Repository (Developer Access) git clone
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