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")):
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("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 | 1.1.7 |
| In Bioconductor since | BioC 3.23 (R-4.6) (0.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.6.0) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VISTA_1.1.7.tar.gz |
| Windows Binary (x86_64) | VISTA_1.1.7.zip |
| macOS Binary (big-sur-x86_64) | VISTA_1.1.7.tgz |
| macOS Binary (sonoma-arm64) | VISTA_1.1.7.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 |