Package: circRNAprofiler 1.27.0

Table of Contents | Introduction | Install the package | Load the package | Running circRNAprofiler | Module 1 - Set up project folder | initCircRNAprofiler() | checkProjectFolder() | Module 2 - Import predicted circRNAs | formatGTF() | getBackSplicedJunctions() | Module 3 - Merge commonly identified circRNAs | mergeBSJunctions() | Module 4 - Filter circRNAs | filterCirc() | Module 5 - Find differentially expressed circRNAs | getDeseqRes() | getEdgerRes() | Module 6 - Map BSJ coordinates between species and genome assemblies | liftBSJcoords() | Module 7 - Annotate circRNAs internal structure and flanking introns | annotateBSJs() | Module 8 - Generate random BSJs | getRandomBSJunctions() | Retrieve target sequences | Module 9 - Retrieve internal circRNA sequences | getCircSeqs() | Module 10 - Retrieve BSJ sequences | getSeqsAcrossBSJs() | Module 11 - Retrieve sequences flanking the BSJs | getSeqsFromGRs() | Screen target sequences | Module 12 - Screen target sequences for RBP/de Novo motifs | getMotifs() | mergeMotifs() | Module 13 - Screen circRNA sequences for miRNA binding sites | getMiRsites() | rearrageMiRres() | Annotate target sequences | Module 14 - Annotate GWAS SNPs | annotateSNPsGWAS() | Module 15 - Annotate repetitive elements | annotateRepeats() | Support | Citation | Acknowledgement | Note | References