Package: VISTA
Type: Package
Title: Visualization and Integrated System for Transcriptomic Analysis
Version: 1.1.7
Authors@R: c(
    person(given = "Chirag", family = "Parsania", email = "chirag.parsania@gmail.com",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4873-2385"))
  )
Description: 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.
License: GPL-3
Encoding: UTF-8
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
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
URL: https://github.com/cparsania/VISTA,
        https://cparsania.github.io/VISTA/
BugReports: https://github.com/cparsania/VISTA/issues
biocViews: RNASeq, DifferentialExpression, GeneExpression,
        Transcriptomics, Visualization
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
LazyData: false
Config/testthat/edition: 3
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-22 01:21:28 UTC
RemoteUrl: https://github.com/bioc/VISTA
RemoteRef: HEAD
RemoteSha: 283ac73bb057141e28cc973d969f9556a269a60c
NeedsCompilation: no
Packaged: 2026-10-22 19:40:54 UTC; root
Author: Chirag Parsania [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4873-2385>)
Maintainer: Chirag Parsania <chirag.parsania@gmail.com>