CircLab

A comprehensive software tool for circRNA detection, function prediction, functional enrichment, and visualization.

Install

- Open dist to download the .whl file and install it by pip

  pip install circlab-0.1.0-py3-none-any.whl

- Download whole project by git

  git clone https://github.com/LiLab-SNNU/CircLab.git

Use Circlab -h to check.

Use

1. ​CircRNA Detection

• We construct a circRNA detection pipeline by snakemake, there are 20 rules in this pipeline which contain fastp, four algorithms to detect, merge.
  • Integrates multiple detection algorithms (e.g., STAR+CIRCexplorer2, BWA+CIRI2, Bowtie2+find_circ).
  • Reduces false positives by combining results from multiple tools.
  • Supports both single-end and paired-end sequencing data.

     CircLab detection -h 
     CircLab detection -i -g data/genome/aragenome.fa -i data/raw.fastq/Ath/Ath_simu_1.fq,data/raw.fastq/Ath/Ath_simu_2.fq -a data/gene.gtf -o outfile 
  

  

2. ​Functional Prediction

   • Predicts circRNA-miRNA-mRNA interaction networks.

      CircLab function miRNA
   

   • Identifies conserved circRNAs across species using sequence alignment and conservation matrix analysis.

      CircLab function conservation 
   

3. ​Visualization

   • Provides six visualization functions, including circRNA length distribution, junction reads, tissue-specific expression, and codon composition.

4. ​Gene Annotation

   • Performs GO and KEGG enrichment analysis for circRNA parent genes.
   • Outputs structured tables and visualizations for downstream analysis.