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bandle

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

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

Bioconductor version: Development (3.18)

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods 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 "4.3") 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")
Analysing differential localisation experiments with BANDLE: Vignette 1 HTML R Script
Analysing differential localisation experiments with BANDLE: Vignette 2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Classification, Clustering, DataImport, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software
Version 1.5.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
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
Linking To Rcpp, RcppArmadillo, BH
Suggests coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling
System Requirements
Enhances
URL http://github.com/ococrook/bandle
Bug Reports https://github.com/ococrook/bandle/issues
See More
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_1.5.0.tar.gz
Windows Binary bandle_1.5.0.zip
macOS Binary (x86_64) bandle_1.5.0.tgz
macOS Binary (arm64) bandle_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bandle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bandle
Bioc Package Browser https://code.bioconductor.org/browse/bandle/
Package Short Url https://bioconductor.org/packages/bandle/
Package Downloads Report Download Stats