VISTA
This is the released version of VISTA; for the devel version, see VISTA.
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("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")
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 | 1.0.0 |
| 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 |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | VISTA_1.0.0.zip |
| 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 |