bandle

DOI: 10.18129/B9.bioc.bandle    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see bandle.

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

Bioconductor version: 3.15

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>

Installation

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

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

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	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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
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_1.0.0.tar.gz
Windows Binary	bandle_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	bandle_1.0.0.tgz
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