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oneSENSE

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

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


Bioconductor version: Development (3.19)

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>

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

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

Details

biocViews DimensionReduction, FlowCytometry, GUI, ImmunoOncology, Software
Version 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>=3)
Depends R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
Imports Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package oneSENSE_1.25.0.tar.gz
Windows Binary
macOS Binary (x86_64) oneSENSE_1.25.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/oneSENSE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oneSENSE
Bioc Package Browser https://code.bioconductor.org/browse/oneSENSE/
Package Short Url https://bioconductor.org/packages/oneSENSE/
Package Downloads Report Download Stats