VISTA (original) (raw)
This is the released version of VISTA; for the devel version, seeVISTA.
Visualization and Integrated System for Transcriptomic Analysis
Bioconductor version: Release (3.23)
The VISTA (Visualization and Integrated System for Transcriptomic Analysis) platform streamlines differential expression workflows by wrapping DESeq2 and edgeR into a SummarizedExperiment-based container with consistent metadata. The package includes visualization utilities, MSigDB enrichment helpers, and optional deconvolution support to simplify interactive exploration of RNA-seq experiments.
Author: Chirag Parsania [aut, cre]
Maintainer: Chirag Parsania <chirag.parsania at gmail.com>
Citation (from within R, enter citation("VISTA")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VISTA")
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("VISTA")Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Software, Transcriptomics, Visualization |
|---|---|
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.3) |
| Imports | AnnotationDbi, cli, clusterProfiler, colorspace, DESeq2, dplyr, edgeR, forcats, ggplot2, ggrepel, GGally, ggpubr, grid, matrixStats, methods, msigdbr, limma, purrr, rlang, S4Vectors, scales, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, viridis |
| System Requirements | |
| URL | https://github.com/cparsania/VISTA https://cparsania.github.io/VISTA/ |
| Bug Reports | https://github.com/cparsania/VISTA/issues |
See More
| Suggests | airway, BiocStyle, circlize, ComplexHeatmap, DT, EnhancedVolcano, ggpointdensity, ggridges, ggalluvial, ggcorrplot, ggrain, ggvenn, enrichplot, knitr, magrittr, patchwork, org.Hs.eg.db, org.Mm.eg.db, quarto, rmarkdown, yaml, writexl, testthat (>= 3.0.0), uwot, xCell2 |
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| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VISTA_1.0.0.tar.gz |
|---|---|
| Windows Binary (x86_64) | VISTA_1.0.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | VISTA_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | VISTA_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VISTA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VISTA |
| Bioc Package Browser | https://code.bioconductor.org/browse/VISTA/ |
| Package Short Url | https://bioconductor.org/packages/VISTA/ |
| Package Downloads Report | Download Stats |