NEWS

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VISTA 0.99.8

VISTA 0.99.7

VISTA 0.99.6

VISTA 0.99.5

• Added read_vista_counts(), read_vista_metadata(), and match_vista_inputs() to standardize common RNA-seq input formats without changing the existing create_vista() API.
• Added derive_vista_metadata() to bootstrap starter sample metadata from count-derived sample names using split- or regex-based parsing.
• Added lightweight import support for plain count tables, featureCounts, STAR gene counts, HTSeq-count, tximport-like inputs, and RSEM gene result files.

VISTA 0.99.4

VISTA 0.99.3

VISTA 0.99.2

VISTA 0.99.1

• example_vista() now uses a precomputed default object to reduce example, test, and package-check runtime while preserving the existing API.

VISTA 0.99.0

Submitted to Bioconductor 2026-02-11

Overview

VISTA (Visualization Toolkit for Transcriptomic Analysis) provides a unified S4-based framework for differential expression analysis of RNA-seq data, wrapping DESeq2 and edgeR workflows with consistent metadata management and rich visualization capabilities.

Key Features

Core Infrastructure

• S4 VISTA class extending SummarizedExperiment for standardized data management
• Unified differential expression workflow supporting DESeq2 and edgeR backends
• Consistent metadata structure for comparisons, cutoffs, and group information
• Flexible color palette system for visualizations

Visualization Suite (28+ functions)

• Dimension reduction: PCA, MDS plots with customizable aesthetics
• DE results: Volcano plots, MA plots, DEG count barplots
• Expression: Barplots, boxplots, violin plots, density plots, joyplots, heatmaps
• Comparisons: Venn diagrams, alluvial plots, correlation heatmaps, pairwise plots
• Fold-change: Scatter plots, barplots, matrix visualizations, chromosome plots

Functional Analysis

• MSigDB enrichment with flexible ID mapping (SYMBOL, ENSEMBL, ENTREZID)
• GO enrichment analysis (BP, MF, CC ontologies)
• KEGG pathway enrichment
• GSEA support with customizable gene sets
• Integrated visualization functions for enrichment results

Optional Features

• Cell-type deconvolution via xCell2 integration
• Automated report generation with Quarto
• Accessor functions for all metadata components

Implementation Details

• Comprehensive input validation and edge case handling
• Extensive test suite (>70% coverage)
• Complete roxygen2 documentation with runnable examples
• BiocStyle vignettes demonstrating complete workflows
• Proper namespace management and import declarations

Bug Fixes

• Fixed contradictory roxygen documentation markers in internal utilities
• Added missing @importFrom declarations across all modules
• Improved error messages for invalid inputs
• Enhanced edge case handling in visualization functions
• Heatmap utilities now validate non-character genes input explicitly, support minimal-call defaults, and allow custom colours for multi-column annotations
• DEG count pie/donut plots now optionally include non-DE genes as an "Other" slice and support configurable label text colour
• get_genes_by_regulation() now supports top-gene ranking by abs(log2fc) and optional annotated table output
• PCA/MDS/UMAP plots now accept the standardized use_group_colors argument while keeping use_vista_colors as a deprecated compatibility alias

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