Overview

• 1. Overview

Installation

• 1. Installation
  • 1.1. Prerequisites
  • 1.2. R libraries required
  • 1.3. Python packages required
  • 1.4. Install bhive
  • 1.5. Upgrade bhive

Change log

• 1. bhive Release history
  • 1.1. Version 1.0.0

Test Dataset

• 1. Testing dataset
  • 1.1. Download raw data
  • 1.2. Convert BAM to FASTQ
  • 1.3. Run CellRanger count workflow
  • 1.4. Run CellRanger aggr workflow
  • 1.5. References

Usage Information

• 1. BC_edit_matrix.py
  • 1.1. Description
  • 1.2. Options
  • 1.3. Input file format
  • 1.4. Example (Visualize sample barcode)
  • 1.5. out put files
• 2. cell_calling.py
  • 2.1. Description
  • 2.2. Example
  • 2.3. Output files
• 3. map_stat.py
  • 3.1. Description
  • 3.2. Example
• 4. seq_logo.py
  • 4.1. Description
  • 4.2. Options
  • 4.3. Input file format
  • 4.4. Example (Visualize sample barcode)
  • 4.5. Example (Visualize cell barcode and UMI)
• 5. seq_qual.py
  • 5.1. Description
  • 5.2. Options
  • 5.3. Example
  • 5.4. Output files

Liscense

• LICENSE

Reference

• Reference