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 (3.24)
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("bandle")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Classification, Clustering, DataImport, ImmunoOncology, MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) |
| System Requirements | |
| URL | http://github.com/ococrook/bandle |
| Bug Reports | https://github.com/ococrook/bandle/issues |
See More
| Suggests | testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling |
| Linking To | Rcpp, RcppArmadillo, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | bandle_1.17.0.tar.gz |
| Windows Binary (x86_64) | bandle_1.17.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | bandle_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | bandle_1.17.0.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 |