{"repo":"nf-core/circrna","free":true,"listed":false,"github":"https://github.com/nf-core/circrna","clone":"git clone https://github.com/nf-core/circrna.git","description":"circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data","language":"Nextflow","stars":61,"topics":["circrna","circrna-prediction","circrna-pipeline","circular-rna","rna-seq","nf-core","nextflow","pipeline","workflow","bioinformatics"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/circrna is a bioinformatics pipeline to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs. The pipeline is still under development, but the BSJ detection and quantification steps are already implemented and functional. The following features are planned to be implemented soon: - Isoform-level circRNA detection and quantification - circRNA-miRNA interaction analysis using SPONGE and spongEffects - Improved downstream analyses If you want to contribute, feel free to create an issue or pull request on the GitHub repository or join the Slack channel. Pipeline summary - Raw read QC ( FastQC ) - Adapter trimming ( Trim Galore! ) - BSJ detection - CIRIquant - STAR 2-Pass mode - CIRCexplorer2 - circRNA finder - DCC - find circ - MapSplice - Segemehl - circRNA annotation - Based on a GTF file - Based on database files (if provided) - Extract circRNA sequences and build circular transcriptome - Merge circular transcriptome with linear transcriptome derived from provided GTF - Quantification of combined circular and linear transcriptome - psirc-quant - miRNA binding affinity analysis (only if the mature parameter is provided) - Normalizes miRNA expression (only if the mirna expression parameter is provided) - Binding site ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/circrna/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}