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oneSENSE

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

Bioconductor version: Release (3.17)

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 "4.3") and enter: 

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

BiocManager::install("oneSENSE")

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

Documentation

Reference Manual PDF

Details

biocViews DimensionReduction, FlowCytometry, GUI, ImmunoOncology, Software
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL (>=3)
Depends R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
Imports Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore
Linking To
Suggests knitr, rmarkdown
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64) oneSENSE_1.22.0.tgz
macOS Binary (arm64) oneSENSE_1.21.0.tgz
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