SubCellBarCode

DOI: 10.18129/B9.bioc.SubCellBarCode    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SubCellBarCode.

SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Bioconductor version: 3.13

Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.

Author: Taner Arslan

Maintainer: Taner Arslan <taner.arslan at ki.se>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("SubCellBarCode")

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("SubCellBarCode")

 

HTML	R Script	SubCellBarCode R Markdown vignettes
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, MassSpectrometry, Proteomics, Software
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL-2
Depends	R (>= 3.6)
Imports	Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
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	SubCellBarCode_1.8.0.tar.gz
Windows Binary	SubCellBarCode_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	SubCellBarCode_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SubCellBarCode
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SubCellBarCode
Package Short Url	https://bioconductor.org/packages/SubCellBarCode/
Package Downloads Report	Download Stats