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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |
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) | |
| 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 |