Sconify

DOI: 10.18129/B9.bioc.Sconify    

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

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Sconify")

Documentation

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, MultipleComparison, SingleCell, Software, Visualization
Version 1.0.0
License Artistic-2.0
Depends R (>= 3.5)
Imports tibble, dplyr, rflann, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr
LinkingTo
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package Sconify_1.0.0.tar.gz
Windows Binary Sconify_1.0.0.zip
Mac OS X 10.11 (El Capitan) Sconify_1.0.0.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 http://bioconductor.org/packages/Sconify/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: