CIRI-cookbook
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CIRI2
About
Usage
An example of running CIRI2
Test of CIRI2
Q&A
CIRI-AS
About
Usage
An example of running CIRI-AS
CIRI-full
About
Installation
Running CIRI-full pipeline
Running CIRI-full step-by-step
Running CIRI-vis
How to run the test data set using CIRI-full
CIRI-vis
About
Installation
Commands and Arguments
Example Usage
CIRIquant
About
Installation
Usage 1: circRNA quantifcation
Usage 2: RNase R effect correction
Usage 3: Differential expression analysis
Test data
CIRI-long
About
Installation
Usage
CIRI-long Sequencing Protocol
CIRI-long Nanopore Library Preparation
circAtlas
circAtlas v2.0
CIRI-cookbook
Docs
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Welcome to CIRI Toolkit’s documentation!
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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
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