bandle
An R package for the Bayesian analysis of differential subcellular localisation experiments
Bioconductor version: 3.23 · Package version: 1.16.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bandle")Details
| Maintainer | Oliver M. Crook <oliver.crook@stats.ox.ac.uk> |
| Author | Oliver M. Crook [aut, cre] (ORCID: <https://orcid.org/0000-0001-5669-8506>), Lisa Breckels [aut] (ORCID: <https://orcid.org/0000-0001-8918-7171>) |
| License | Artistic-2.0 |
| URL | http://github.com/ococrook/bandle |
| Bug Reports | https://github.com/ococrook/bandle/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, Classification, Clustering, DataImport, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software |
| Package Short Url | https://bioconductor.org/packages/bandle/ |
Citation
From within R, enter citation("bandle"):
Oliver M. Crook, Lisa Breckels. bandle: An R package for the Bayesian analysis of differential subcellular localisation experiments. doi:10.18129/B9.bioc.bandle, R package version 1.16.0, https://bioconductor.org/packages/bandle.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Vignette 1: Getting Started with BANDLE
- Vignette 2: A workflow for analysing differential localisation
Download
Follow the installation instructions to use this package in your R session.
| Source package | bandle_1.16.0.tar.gz |
| Windows binary (x86_64) | bandle_1.16.0.zip |
| macOS binary (arm64) | bandle_1.16.0.tgz |
| macOS binary (x86_64) | bandle_1.16.0.tgz |
Dependencies
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, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4)
LinkingTo: Rcpp, RcppArmadillo, BH
Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling