Welcome to CIRI Toolkit’s documentation!

CIRI2

• About
  • Release Notes
  • Citations:
• Usage
  • Commands and arguments
  • Preparation for using CIRI2
  • Annotation formats
• An example of running CIRI2
• Test of CIRI2
• Q&A

CIRI-AS

• About
• Usage
  • How to run CIRI-AS
  • Commands and arguments
  • Preparation for using CIRI-AS
  • Annotation formats
• An example of running CIRI-AS

CIRI-full

• About
• Installation
• Running CIRI-full pipeline
• Running CIRI-full step-by-step
  • The RO1 module
  • The RO2 module
  • The Merge module
• Running CIRI-vis
• How to run the test data set using CIRI-full

CIRI-vis

• About
  • Author
  • Release Notes
• Installation
  • Prerequisites
  • Install CIRI-vis
• Commands and Arguments
  • Running CIRI-vis
  • Output files
• Example Usage

CIRIquant

• About
  • Author
  • Release Notes
  • License
  • Citing CIRIquant
• Installation
  • Prerequisites
  • Use the released version (Recommended)
  • Install CIRIquant and dependencies using conda (Not recommended)
  • Install CIRIquant using pip
  • Install CIRIquant from source code
• Usage 1: circRNA quantifcation
  • Basic options
  • Example YAML config
  • Example circRNA bed file
  • Example Usage
  • Output format
• Usage 2: RNase R effect correction
  • Example usage
• Usage 3: Differential expression analysis
  • Study without biological replicate
  • Study with biological replicates
• Test data
  • Download test dataset
  • circRNA quantification
  • Differential expression analysis

CIRI-long

• About
  • CIRI-long: circular RNA identifier using long-read sequencing data
  • Author
  • Release Notes
  • License
  • Citing CIRI-long
• Installation
  • Dependency
  • Install CIRI-long from source code
  • Install CIRI-long using pip
• Usage
  • Basic usage
  • Step1. circRNA identification
  • Step2. isoform collapse
  • Step3. Output visualization

CIRI-long Sequencing Protocol

• CIRI-long Nanopore Library Preparation
  • 1. Total RNA Extraction & Ribosomal RNA Depletion
  • 2. Poly(A) Tailing & RNase R Treatment
  • 3. SMARTer Reverse Transcription
  • 4. cDNA PCR Amplification
  • 5. Fragment Size Selection
  • 6. Nanopore Sequencing

circAtlas

• circAtlas v2.0