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Sconify

This is the development version of Sconify; for the stable release version, see Sconify.

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


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Sconify")

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

Documentation

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

browseVignettes("Sconify")
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

Details

biocViews FlowCytometry, ImmunoOncology, MultipleComparison, SingleCell, Software, Visualization
Version 1.23.0
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
System Requirements
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Suggests knitr, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Sconify_1.23.0.tar.gz
Windows Binary Sconify_1.23.0.zip
macOS Binary (x86_64) Sconify_1.23.0.tgz
macOS Binary (arm64) Sconify_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Sconify
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Sconify
Bioc Package Browser https://code.bioconductor.org/browse/Sconify/
Package Short Url https://bioconductor.org/packages/Sconify/
Package Downloads Report Download Stats