Package: VISTA 1.0.0

Chirag Parsania

VISTA: Visualization and Integrated System for Transcriptomic Analysis

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.

Authors:Chirag Parsania [aut, cre]

VISTA_1.0.0.tar.gz
VISTA_1.0.0.zip(r-4.7)VISTA_1.0.0.zip(r-4.6)VISTA_1.0.0.zip(r-4.5)
VISTA_1.0.0.tgz(r-4.6-any)VISTA_1.0.0.tgz(r-4.5-any)
VISTA_1.0.0.tar.gz(r-4.7-any)VISTA_1.0.0.tar.gz(r-4.6-any)
VISTA_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
VISTA/json (API)
NEWS

# Install 'VISTA' in R:
install.packages('VISTA', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cparsania/vista/issues

Pkgdown/docs site:https://cparsania.github.io

Datasets:
  • count_data - Example RNA-seq count matrix shipped with VISTA
  • sample_metadata - Sample metadata accompanying the VISTA airway example counts

On BioConductor:VISTA-1.1.0(bioc 3.24)VISTA-1.0.0(bioc 3.23)

rnaseqdifferentialexpressiongeneexpressiontranscriptomicsvisualization

5.54 score 7 stars 244 downloads 77 exports 191 dependencies

Last updated from:d7e91e75f3 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE422
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source / vignettesOK599
linux-release-x86_64NOTE641
macos-release-arm64NOTE357
macos-oldrel-arm64NOTE299
windows-develNOTE503
windows-releaseNOTE415
windows-oldrelNOTE531
wasm-releaseOK283

Exports:as_vistabenchmark_vista_equivalencecomparisonscreate_vistacutoffsdeg_summaryderive_vista_metadataenrichMsigDBexample_vistaexport_vista_assetsget_cell_fractionsget_celltype_barplotget_celltype_group_dotplotget_celltype_heatmapget_corr_heatmapget_deg_alluvialget_deg_count_barplotget_deg_count_donutplotget_deg_count_pieplotget_deg_venn_diagramget_enrichment_chordget_enrichment_plotget_expression_barplotget_expression_boxplotget_expression_chromosome_plotget_expression_densityget_expression_heatmapget_expression_joyplotget_expression_lineplotget_expression_lollipopget_expression_matrixget_expression_raincloudget_expression_scatterget_expression_violinplotget_foldchange_barplotget_foldchange_boxplotget_foldchange_chromosome_plotget_foldchange_heatmapget_foldchange_lineplotget_foldchange_lollipopget_foldchange_matrixget_foldchange_raincloudget_foldchange_scatterget_genes_by_regulationget_go_enrichmentget_gseaget_kegg_enrichmentget_ma_plotget_mds_plotget_msigdb_enrichmentget_pairwise_corr_plotget_pathway_genesget_pathway_heatmapget_pca_plotget_umap_plotget_volcano_plotgroup_colorsgroup_palettematch_vista_inputsnorm_countsread_vista_countsread_vista_metadatarow_datarun_cell_deconvolutionrun_deseq_analysisrun_edger_analysisrun_limma_analysisrun_vista_reportsample_infosave_vista_datasave_vista_plotset_de_sourceset_rowdataset_vista_comparison_colorsset_vista_group_colorsvalidate_vistavalidate_vista_deep

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassassertthatbabelgenebackportsbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbootbroombslibcachemcallrcarcarDatacliclusterclusterProfilercodetoolscolorspacecorrplotcowplotcpp11crayoncurlDBIDelayedArrayDerivDESeq2digestdoByDOSEdplyredgeRenrichitenrichplotevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesGGallyggforceggfunggiraphggnewscaleggplot2ggplotifyggpubrggrepelggsciggsignifggstatsggtangleggtreeglueGO.dbGOSemSimgridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmsigdbrnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigplyrpngpolyclippolynomprettyunitsprocessxprogresspspurrrquantregqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrmarkdownRSQLiterstatixS4ArraysS4VectorsS7sassscalesscatterpieSeqinfosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidydrtidyrtidyselecttidytreetimeDatetinytextreeiotweenrurcautf8vctrsviridisviridisLitewithrxfunXVectoryamlyulab.utilszoo

Complete RNA-seq Analysis Workflow with VISTA

VISTA Development Team

Rendered fromVISTA-airway.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-04-09
Started: 2026-02-17

Readme and manuals

Help Manual

Help pageTopics
Coerce SummarizedExperiment to VISTAas_vista
Benchmark VISTA against standalone differential-expression backendsbenchmark_vista_equivalence
Example RNA-seq count matrix shipped with VISTAcount_data
Create a VISTA Object with Internal DE Analysiscreate_vista
Derive starter sample metadata from count sample namesderive_vista_metadata
Perform MSigDB over-representation analysis on a VISTA objectenrichMsigDB enrichMsigDB,VISTA-method
Build a small example VISTA objectexample_vista
Export a complete VISTA asset bundleexport_vista_assets
Retrieve stored cell fraction estimatesget_cell_fractions
Plot cell-type composition as stacked barsget_celltype_barplot
Plot group-level deconvolution scores as dot plotget_celltype_group_dotplot
Plot cell-type deconvolution heatmapget_celltype_heatmap
Draw a sample correlation heatmapget_corr_heatmap
Plot alluvial diagram showing gene regulation transitions across comparisonsget_deg_alluvial
Barplot of DEG counts (Up/Down) across comparisonsget_deg_count_barplot
Donut chart of DEG counts (Up/Down) across comparisonsget_deg_count_donutplot
Pie chart of DEG counts (Up/Down) across comparisonsget_deg_count_pieplot
DEG Venn diagramget_deg_venn_diagram
Chord diagram of enrichment gene-pathway relationshipsget_enrichment_chord
Plot enrichment results using -log10(FDR)get_enrichment_plot
Plot gene expression as barplotsget_expression_barplot
Plot gene expression distributions as boxplotsget_expression_boxplot
Chromosome plot for expressionget_expression_chromosome_plot
Plot expression distributions as density curvesget_expression_density
Expression heatmapget_expression_heatmap
Plot expression distributions as ridgelinesget_expression_joyplot
Gene expression line plotget_expression_lineplot
Plot expression as a lollipop chartget_expression_lollipop
Retrieve an expression matrix from a VISTA objectget_expression_matrix
Raincloud plot of expression valuesget_expression_raincloud
Compare normalized expression between two samples or groupsget_expression_scatter
Violin plot of expression valuesget_expression_violinplot
Plot fold-change barplots across comparisons for selected genesget_foldchange_barplot
Plot fold-change distributions across comparisonsget_foldchange_boxplot
Chromosome plot for fold changeget_foldchange_chromosome_plot
Fold-change heatmapget_foldchange_heatmap
Fold-change line plot across comparisonsget_foldchange_lineplot
Fold-change plotting helpers (overview)get_foldchange_lollipop
Extract a log2 fold-change matrixget_foldchange_matrix
Raincloud plot of fold-change distributions across comparisonsget_foldchange_raincloud
Fold-change scatterplot between two comparisonsget_foldchange_scatter
Get Genes by Regulationget_genes_by_regulation
Run GO enrichment directly from a VISTA comparisonget_go_enrichment
Gene set enrichment analysis (GSEA) from a VISTA comparisonget_gsea
Run KEGG enrichment directly from a VISTA comparisonget_kegg_enrichment
Generate MA plot from a VISTA objectget_ma_plot
Generate an MDS plot for samples in a VISTA objectget_mds_plot
Run MSigDB enrichment directly from a VISTA comparisonget_msigdb_enrichment
Plot pairwise correlations between samplesget_pairwise_corr_plot
Extract genes from enriched pathwaysget_pathway_genes
Plot pathway-specific expression heatmaps from enrichment outputget_pathway_heatmap
PCA plotget_pca_plot
Generate a UMAP plot for samples in a VISTA objectget_umap_plot
Generate a volcano plot for a comparison in a VISTA objectget_volcano_plot
Match count and metadata inputs for VISTAmatch_vista_inputs
Print a VISTA object like a SummarizedExperimentprint.VISTA print.vista
Read and standardize count inputs for VISTAread_vista_counts
Read and standardize sample metadata for VISTAread_vista_metadata
Run Cell Deconvolution on Bulk RNA-seq from VISTA Objectrun_cell_deconvolution
Run Differential Expression Analysis with DESeq2, edgeR, or limma-voomrun_deseq_analysis run_edger_analysis run_limma_analysis
Generate a publication-ready VISTA workflow reportrun_vista_report
Sample metadata accompanying the VISTA airway example countssample_metadata
Save VISTA tabular outputs to disksave_vista_data
Save a VISTA plot object to disksave_vista_plot
Set active DE source in a VISTA objectset_de_source
Set or append rowData annotations on a VISTA objectset_rowdata
Set manual comparison colors in a VISTA objectset_vista_comparison_colors
Set manual group colors in a VISTA objectset_vista_group_colors
Validate a VISTA objectvalidate_vista
Deep validation of VISTA differential-expression fidelityvalidate_vista_deep
Accessor Methods for VISTA Objectcomparisons comparisons,VISTA-method cutoffs cutoffs,VISTA-method deg_summary deg_summary,VISTA-method group_colors group_colors,VISTA-method group_palette group_palette,VISTA-method norm_counts norm_counts,VISTA-method row_data row_data,VISTA-method sample_info sample_info,VISTA-method VISTA-accessors
VISTA S4 Class DefinitionVISTA-class