SimiCviz
This is the development version of SimiCviz; to use it, please install the devel version of Bioconductor.
Visualization Tools for Gene Regulatory Network Analysis
Bioconductor version: Development (3.24)
Visualization and export utilities for SimiC and SimiCPipeline outputs. The package focuses on importing SimiC-style results (e.g., weights, AUC metrics) from pickle/CSV files, processing and generating publication-ready plots (networks, heatmaps, distributions) and tables saved into a reproducible, ordered directory hierarchy.
Author: Irene Marín-Goñi [aut, cre]
Maintainer: Irene Marín-Goñi <imarin.4 at alumni.unav.es>
citation("SimiCviz")):
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("SimiCviz")
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("SimiCviz")| SimiCviz: Visualization and Analysis of Gene Regulatory Networks | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneRegulation, Network, NetworkInference, SingleCell, Software, Visualization |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6) |
| Imports | methods, stats, BiocParallel, viridisLite, utils, Matrix, graphics, SummarizedExperiment, colorspace, gridExtra, ggplot2, dplyr, tibble, tidyr, reshape2, scales, reticulate (>= 1.45.0) |
| System Requirements | Python (>= 3.8) |
| URL | https://github.com/ML4BM-Lab/SimiCviz |
| Bug Reports | https://github.com/ML4BM-Lab/SimiCviz/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| 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 | SimiCviz_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | SimiCviz_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | SimiCviz_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SimiCviz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SimiCviz |
| Bioc Package Browser | https://code.bioconductor.org/browse/SimiCviz/ |
| Package Short Url | https://bioconductor.org/packages/SimiCviz/ |
| Package Downloads Report | Download Stats |