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Welcome to the UMIche site!

A comprehensive platform for UMI-associated analysis.

Features

• UMI method repertoire - comprehensive methods for UMI deduplication
• UMI deduplication pipeline - pipelines for UMI deduplication effects in demultiplexing
• UMI count simulation - train and simulate scRNA-seq UMI count matrix
• UMI visualisation - graph representation and plots of UMI deduplication-related data

Commands

• umiche.graph - UMI graph with nodes and edges
• umiche.dedup - UMI deduplication methods
• umiche.homotrimer - Collapsing or splitting homotrimer UMIs
• umiche.trim - Extraction of UMIs and other read components
• umiche.io - File I/O
• umiche.mat - UMI count matrix simulation
• umiche.pipeline - UMI deduplication pipeline one-stop
• umiche.plot - Plot UMIs in graphs or lines

Platform

• PyPI
  pip install umiche
• Conda
  conda install jianfeng_sun::umiche
• Docker
  docker pull 2003100127/umiche
• Github
  git clone https://github.com/2003100127/umiche.git