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>

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

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
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
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/
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