SubCellBarCode

This is the released version of SubCellBarCode; for the devel version, see SubCellBarCode.

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

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DOI: 10.18129/B9.bioc.SubCellBarCode

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, MassSpectrometry, Proteomics, Software

Version 1.26.0

In Bioconductor since BioC 3.9 (R-3.6) (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

URL

Suggests knitr, rmarkdown, BiocStyle

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Package Archives

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

Source Package SubCellBarCode_1.26.0.tar.gz

Windows Binary (x86_64) SubCellBarCode_1.26.0.zip

macOS Binary (x86_64) SubCellBarCode_1.26.0.tgz

macOS Binary (arm64) SubCellBarCode_1.26.0.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/

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