bandle

DOI: 10.18129/B9.bioc.bandle    

This is the development version of bandle; for the stable release version, see bandle.

An R package to for the Bayesian analysis of differential subcellular localisation experiments

Bioconductor version: Development (3.16)

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental method supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

Author: Oliver M. Crook [aut, cre] , Lisa Breckels [aut]

Maintainer: Oliver M. Crook <oliver.crook at stats.ox.ac.uk>

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

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("bandle")

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("bandle")

 

HTML R Script Analysing differential localisation experiments with BANDLE: Vignette 1
HTML R Script Analysing differential localisation experiments with BANDLE: Vignette 2
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, Classification, Clustering, DataImport, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version 1.1.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc
Imports Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang
LinkingTo Rcpp, RcppArmadillo, BH
Suggests coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling
SystemRequirements
Enhances
URL http://github.com/ococrook/bandle
BugReports https://github.com/ococrook/bandle/issues
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 bandle_1.1.0.tar.gz
Windows Binary bandle_1.1.0.zip (64-bit only)
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/bandle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bandle
Package Short Url https://bioconductor.org/packages/bandle/
Package Downloads Report Download Stats

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