oneSENSE

DOI: 10.18129/B9.bioc.oneSENSE    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see oneSENSE.

One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)

Bioconductor version: 3.9

A graphical user interface that facilitates the dimensional reduction method based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm, for categorical analysis of mass cytometry data. With One-SENSE, measured parameters are grouped into predefined categories, and cells are projected onto a space composed of one dimension for each category. Each dimension is informative and can be annotated through the use of heatplots aligned in parallel to each axis, allowing for simultaneous visualization of two catergories across a two-dimensional plot. The cellular occupancy of the resulting plots alllows for direct assessment of the relationships between the categories.

Author: Cheng Yang, Evan Newell, Yong Kee Tan

Maintainer: Yong Kee Tan <yongkee.t at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("oneSENSE")

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("oneSENSE")

 

HTML	R Script	Introduction to oneSENSE GUI
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DimensionReduction, FlowCytometry, GUI, ImmunoOncology, Software
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	GPL (>=3)
Depends	R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
Imports	Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	oneSENSE_1.6.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	oneSENSE_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/oneSENSE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/oneSENSE
Package Short Url	https://bioconductor.org/packages/oneSENSE/
Package Downloads Report	Download Stats