oneSENSE
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see oneSENSE.
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
Bioconductor version: 3.12
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("oneSENSE")):
Installation
To install this package, start R (version "4.0") 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
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction, FlowCytometry, GUI, ImmunoOncology, Software |
| Version | 1.12.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | oneSENSE_1.12.0.tar.gz |
| Windows Binary | oneSENSE_1.12.0.zip |
| macOS 10.13 (High Sierra) | oneSENSE_1.12.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |