bandle

DOI: 10.18129/B9.bioc.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>

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

PDF		Reference Manual

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 year)
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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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