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SubCellBarCode

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
SubCellBarCode R Markdown vignettes HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, MassSpectrometry, Proteomics, Software
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
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Suggests knitr, rmarkdown, BiocStyle
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Package Archives

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

Source Package SubCellBarCode_1.18.0.tar.gz
Windows Binary SubCellBarCode_1.18.0.zip
macOS Binary (x86_64) SubCellBarCode_1.18.0.tgz
macOS Binary (arm64) SubCellBarCode_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SubCellBarCode
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SubCellBarCode
Bioc Package Browser https://code.bioconductor.org/browse/SubCellBarCode/
Package Short Url https://bioconductor.org/packages/SubCellBarCode/
Package Downloads Report Download Stats