Sconify

DOI: 10.18129/B9.bioc.Sconify    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	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
PDF		Reference Manual

Details

biocViews	FlowCytometry, ImmunoOncology, MultipleComparison, SingleCell, Software, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	Artistic-2.0
Depends	R (>= 3.5)
Imports	tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	Sconify_1.12.0.tar.gz
Windows Binary	Sconify_1.12.0.zip
macOS 10.13 (High Sierra)	Sconify_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Sconify
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Sconify
Package Short Url	https://bioconductor.org/packages/Sconify/
Package Downloads Report	Download Stats