MetaScope

MetaScope is a genome browser with integrative functions and a highly flexible, interactive user interface, by which molecular biologists with minimal computational skills can visualize their genome-scale datasets along with canonical genomic annotations, and analyze, curate and integrate with data operation functions of MetaScope. The datasets MetaScope can handle include tiling array data (ChIP-chip and expression profiling), calculated peak data, transcription start site data, and genomic annotation in GFF format.

Use MetaScope in order to

• Visualize datasets including ChIP-chip data, expression profiling data and transcription start site data
• Analyze, validate, curate and integrate datasets by cross-referencing multiple -omic data
• Build and share genome annotations
• Compare multiple -omics data from two or more species

Download

Platform	Version	Download
Windows x64	v1.1.11 (recommended)	MetaScope_v1.1.11_Windows_x64.zip
Windows x64	v1.2.1	MetaScope_v1.2.1_Windows_x64.zip
macOS Apple Silicon	v1.2.1	MetaScope_v1.2.1_macOS_arm64.zip

Features

• Interactive genomic map with pan, zoom, and feature selection
• GFF / GZ / ZIP file support with automatic read-only mode for large files
• Memory-optimized for datasets with millions of features
• Workspace save/restore with auto-save and crash recovery
• Export to PNG (300 dpi) and SVG
• Docking panel layout with drag-to-reorder tabs
• Single executable deployment (no external dependencies)

Supported File Formats

Format	Mode
.gff	Editable (read-only if >= 20 MB)
.gz / .gzip	Read-only (in-memory decompression)
.zip	Read-only (in-memory decompression)

Keyboard Shortcuts

Navigation

Windows	macOS	Action
Left / Right	Left / Right	Scroll left / right
Shift+Left / Shift+Right	Shift+Left / Shift+Right	Scroll left / right (large)
Home / End	Home / End	Go to genome start / end
Ctrl+G	Cmd+G	Go to position

Zoom

Windows	macOS	Action
Ctrl++ / Ctrl+-	Cmd++ / Cmd+-	Zoom in / out
Ctrl+0	Cmd+0	Zoom to custom level
Ctrl+Scroll	Cmd+Scroll	Zoom in / out (mouse)

File and View

Windows	macOS	Action
Ctrl+O	Cmd+O	Open file
Ctrl+Tab / Ctrl+Shift+Tab	Cmd+Tab / Cmd+Shift+Tab	Next / previous tab
Ctrl+T	Cmd+T	Split view
Ctrl+F	Cmd+F	Search
F5	F5	Refresh view

Track

Windows	macOS	Action
Ctrl+Shift+Up / Down	Cmd+Shift+Up / Down	Move track up / down
Ctrl+Shift+C	Cmd+Shift+C	Set track color
Ctrl+Shift+H	Cmd+Shift+H	Set track height
Ctrl+Shift+B / P / L	Cmd+Shift+B / P / L	Display as bar / point / line

Feature Editing

Windows	macOS	Action
NumPad 1 / Alt+Left	Option+Left	Move feature left
NumPad 2 / Alt+Right	Option+Right	Move feature right
NumPad 4 / Alt+Down	Option+Down	Shrink start
NumPad 5 / Alt+Up	Option+Up	Expand end

Recent Changes

macOS / Windows

v1.2.1

• Platform-specific window chrome: macOS uses system title bar integration, Windows uses standard window frame
• Keyboard shortcuts show Ctrl on Windows, Cmd on macOS

v1.2.0

• macOS Apple Silicon native port using AvaloniaUI (cross-platform -- build for Windows with dotnet publish -r win-x64)
• Drag-to-reorder document tabs with close button
• macOS-native UI redesign

Windows (recommended)

v1.1.11

• Workspace: auto-creates a temporary workspace when opening GFF files, enabling auto-save and crash recovery

v1.1.10

• Auto Save: automatic saving after feature edits (persists across sessions)
• Alt+Arrow keys for feature editing (move, expand, shrink)
• UI/UX improvements and bug fixes

v1.1.9

• Export Image: PNG (300 dpi) and SVG vector export (Ctrl+Shift+E)

v1.1.8

• Feature tooltip on hover (position, score, strand, name)

v1.1.7

• NumPad feature adjustment: move (NumPad 1/2) and resize (NumPad 4/5) for single selected feature
• Read-only track feature selection blocked

v1.1.6

• Recent Files list in File menu (up to 10 files)
• Status bar showing position, zoom level, feature count, and sequence ID
• Read-only threshold increased to 20 MB

v1.1.5

• Keyboard shortcuts: Arrow keys scroll, Home/End navigation, Ctrl+Tab switching, F5 refresh

v1.1.4

• Global exception handlers to prevent silent crashes
• Stream resource leak protection for GZip/ZIP/Save operations
• Parse error logging with skipped line count summary

v1.1.3

• Single executable deployment (AvalonDock embedded)
• Version display in title bar and Introduction page

v1.1.2

• Major memory optimization (~76% reduction for large GFF files)

v1.1.1

• Read-only mode for large files with lock icon indicator
• Compressed file support (.gz, .zip) with in-memory decompression

Build from Source

Windows (.NET Framework 4.8)

Open src/windows/VugMap.sln in Visual Studio 2022+ and build in Release configuration.

Output: VugMap/bin/Release/MetaScope.exe

macOS / Windows (.NET 8+, AvaloniaUI)

cd src/mac
dotnet run --project MetaScope          # Run
dotnet build -c Release                 # Build
dotnet publish -c Release -r osx-arm64 --self-contained  # Publish (macOS)
dotnet publish -c Release -r win-x64 --self-contained    # Publish (Windows)

License

All rights reserved.