VISTA
This is the development version of VISTA; for the stable release version, see VISTA.
Visualization and Integrated System for Transcriptomic Analysis
Bioconductor version: Development (3.24)
VISTA (Visualization and Integrated System for Transcriptomic Analysis) runs bulk RNA-seq differential expression with DESeq2, edgeR or limma-voom, or a DESeq2/edgeR consensus, and keeps counts, results for every contrast, gene annotation, colours and analysis parameters in one validated SummarizedExperiment-derived object. Plotting functions, GO, KEGG and MSigDB enrichment, optional cell-type deconvolution and a Quarto report all read that object, and an exported benchmark checks its results against independent DESeq2, edgeR and limma runs.
Author: Chirag Parsania [aut, cre] 
Maintainer: Chirag Parsania <chirag.parsania at gmail.com>
citation("VISTA")):Chirag Parsania. VISTA: Visualization and Integrated System for Transcriptomic Analysis. doi:10.18129/B9.bioc.VISTA, R package version 1.1.5, https://bioconductor.org/packages/VISTA.
Generated from the package metadata; it may differ from the package's own citation.
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("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")| Complete RNA-seq Analysis Workflow with VISTA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Software, Transcriptomics, Visualization |
| Version | 1.1.5 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | AnnotationDbi, BiocGenerics, cli, clusterProfiler, colorspace, DESeq2, dplyr, edgeR, forcats, ggplot2, ggrepel, GGally, ggpubr, grDevices, graphics, grid, matrixStats, methods, msigdbr, limma, purrr, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, tools, utils |
| 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, codetools, 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VISTA_1.1.5.tar.gz |
| Windows Binary (x86_64) | VISTA_1.1.5.zip |
| macOS Binary (big-sur-x86_64) | VISTA_1.1.5.tgz |
| macOS Binary (sonoma-arm64) | VISTA_1.1.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VISTA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VISTA |
| Package Short Url | https://bioconductor.org/packages/VISTA/ |
| Package Downloads Report | Download Stats |