Welcome

Note

Documentation for v1.8.0 can be found here

Mosaic is a set of tools to analyze DNA and protein data obtained from the Mission Bio Tapestri instrument.

• Introduction
  • Additional resources
  • Need help?
• Installation
  • Detailed Instructions
  • Older versions
• Getting Started
  • Loading a sample
  • Merging h5 files
  • Tutorials
• Data structure
  • Basics
  • DNA
  • CNV
  • Protein

• Index

Vignettes

• Code Snippets
  • Annotate your variants
  • Multi-assay heatmap
  • Fishplot to visualize clonal evolution
  • Group cells by a select number of DNA variants
• Basic usage of mosaic
  • Setup
  • Data Structure
  • DNA Analysis
  • CNV Analysis
  • Protein Analysis
  • Statistical Significance
  • Combined Visualizations
  • Saving
• Manual CNV analysis
  • Filtering amplicons
  • Normalization and ploidy computation
  • Visualizations
• Filtering barcodes and ids
  • Filtering assays
  • Filtering the entire sample
• Plot customizations
  • Reproducible UMAPs
  • Updating the colors for the DNA plots
  • CNV heatmaps
  • Custom multi assay plot
• Multisample analysis
  • Setup
  • Applying functions
  • Drawing figures
  • Multisample plots
• Additional plots and customizations
  • Load in dependencies
  • Load in data
  • GQ violin plots
  • Stacked bar graph for multi-sample analysis
  • Reads per amplicon
  • Count barcodes with at least one mutation
  • Custom cluster order
  • Custom heatmap legend
  • Perform CNV analysis on your data
  • P-value chart per gene
  • Calculate an average P-value per gene
  • Protein read distribution tool
  • Plot a joint scatterplot and histogram
  • CNV signature per chromosome
  • Save output for one clone
• Mosaic analysis walk-through
  • Setup
  • DNA Analysis
  • CNV Analysis
  • Protein Analysis
  • Combined visualizations

Interface

Modules

io	Module to read and write h5 files
utils	Utility functions
constants	Colors and keys for layers and attributes

Classes

_Assay	Abstract class for all assays
Dna	Container for DNA data.
Cnv	Container for CNV data.
Protein	Container for Protein data
Sample	Container for multiple assays.
SampleGroup	A group of samples related to each other