Overview | Key Features | Database Formats | Indexed Format (Recommended) | Per-Chromosome Format (Legacy) | Creating Databases | New Databases (Indexed Format) | Force Legacy Format | Checking Database Format | Converting Databases | Convert Entire Database | Convert Individual Tracks | Convert Intervals | Migration Guide | When to Migrate | Migration Workflow | Copying Tracks Between Databases | Use gtrack.copy() | Round-tripping through a text file | Performance Comparison | Operations Faster with Indexed Format | Operations Similar Performance | Summary | Backward Compatibility | Fully Compatible | Example: Mixed Environment | Troubleshooting | "File descriptor limit reached" | "Track not found after copying files" | "Conversion fails with disk space error" | Best Practices | For New Projects | For Existing Projects

Create misha database from ucsc | hg19 | hg38 | mm9 | mm10 | Import HiC observed contacts

Workflow | Distributed mode | Local mode | Analysis | Spatial contact enrichment - used to measure contact enrichment between two sets of genomic features. | Options | System parameters | Visualization parameters

Create a misha database from UCSC | hg19 | hg38 | mm9 | mm10 | mm39 | Building from UCSC mammal hubs (Zoonomia)

Package 'misha' - User Manual | Genomic Database | Dataset API | Working Database vs Datasets | Track Resolution and Collision Handling | Cross-Database Track Expressions | Querying Track and Interval Sources | Creating and Sharing Datasets | Creating a Linked Database | Unloading Datasets | Moving and Copying Tracks | Virtual Tracks Across Sources | Backward Compatibility | File Formats | chrom_sizes.txt | Seq Files | Indexed Format (Recommended) | Per-Chromosome Format | Track Files | Indexed Format (Recommended for Multi-Contig Genomes) | PSSM Set | PSSM Key | PSSM Data | Intervals | 1D Intervals | 2D Intervals | Interval Sets | Dual Intervals | Serializing Intervals, Big and Small Interval Sets | Interval Set Storage Formats | Tracks | 1D Track | Array Track | 2D Track | Track as an Intervals Set | Track Attributes | Track Variables | Track Attributes vs. Track Variables | Track Expressions | Introduction | Virtual Tracks | Value-Based Tracks | Administrating Virtual Tracks | Track Expression Evaluation under Optimization | Revealing Current Iterator Interval | Iterators | Scope | Band | Random Algorithms | Multitasking | Controlling the Number of Processes | Auto-Configuration | Limiting the Memory Consumption | Other Considerations

The Core Idea | Four Concepts You Need First | 1) Track | 2) Intervals | 3) Iterator | 4) Virtual Track | Minimal Workflow | PWM in One Minute

Introduction | Getting Started | Dense Arrays | Vectors | Matrices | Verifying Zero-Copy | Type Handling | Named Arrays | Named Vectors | Named Matrices | Sparse Matrices | Memory Management | Three-Layer Defense | Explicit Release | Scoped Release | Tuning GC Pressure | Copy-on-Write Semantics | Serialization | Known Limitations

Basic usage | Custom cluster ordering | Missing data | High dimensions | Comparison with R vanilla kmeans | Random seed

'tgstat' package - Tanay's group statistical utilities | Package Configuration | Use of BLAS Library | Multitasking

Introduction | Database | DB dirs, Namespaces and Read-Only Tracks | Load-on-demand vs. Pre-load Modes | Maintaining Database | File and directory permissions | Tracks | Records and References | Categorical and Quantitative Tracks | Logical tracks | Track Attributes | Track Variables | Track Attributes vs. Track Variables | Subsets | Accessing the Data | Track Expressions | Run-time Track Variable is a Vector | Matching Reference in the Track Expression | Virtual Tracks | Iterators | Track Iterator | Id-Time Points Iterator | Ids Iterator | Time Intervals Iterator | Id-Time Intervals Iterator | Beat Iterator | Extended Beat Iterator | Periodic Iterator | Implicit Iterator | Revealing Current Iterator Time | Filters | Named Filters | Other Objects within Filters | Managing Reference in Filters | Advanced Naryn | Random Algorithms | Multitasking | Appendix | R vs. Python Interface Differences | Options | Common Table Formats | Id-Time Points Table | Id-Time Values Table | Ids Table | Time Intervals Table | Id-Time Intervals Table

The Problem | Slanted Matrices | Reordered Clustering | Ordered Clustering