S4Cartographer
This is the development version of S4Cartographer; to use it, please install the devel version of Bioconductor.
Visualize S4 class inheritance across R/Bioconductor packages
Bioconductor version: Development (3.24)
S4 Object-Oriented Programming is fundamental to the Bioconductor ecosystem, enabling modularity and code reuse across hundreds of packages. However, the multi-layered inheritance structures within and between packages can be difficult to navigate. S4Cartographer facilitates the exploration of these relationships by visualizing S4 class hierarchies as directed graphs. By representing classes as nodes and inheritance as edges, it provides a clear overview of complex dependency networks.
Author: Malte Thodberg [cre, aut]
Maintainer: Malte Thodberg <maltethodberg at gmail.com>
citation("S4Cartographer")):
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("S4Cartographer")
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("S4Cartographer")| The S4Cartographer R/Bioconductor package | HTML | R Script |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Software, Visualization |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | methods |
| Imports | ggraph, tidygraph, igraph, ggplot2, checkmate, ggthemes, rlang, BiocBaseUtils, utils |
| System Requirements | |
| URL | https://github.com/MalteThodberg/S4Cartographer |
| Bug Reports | https://github.com/MalteThodberg/S4Cartographer/issues |
See More
| Suggests | BiocSingular, BiocStyle, Biostrings, clusterExperiment, DelayedArray, DESeq2, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges, HDF5Array, InteractionSet, IRanges, knitr, MultiAssayExperiment, ResidualMatrix, rmarkdown, S4Vectors, ScaledMatrix, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, TileDBArray, VCFArray, XVector |
| Linking To | |
| 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 | S4Cartographer_0.99.3.tar.gz |
| Windows Binary (x86_64) | S4Cartographer_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | S4Cartographer_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | S4Cartographer_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/S4Cartographer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/S4Cartographer |
| Bioc Package Browser | https://code.bioconductor.org/browse/S4Cartographer/ |
| Package Short Url | https://bioconductor.org/packages/S4Cartographer/ |
| Package Downloads Report | Download Stats |