├── .gitignore ├── DESCRIPTION ├── InputFilesExample ├── SRR444655.Chimeric.out.junction.gz ├── SRR444655.ReadsPerGene.out.tab.gz ├── SRR444655.SJ.out.tab.gz ├── SRR444655.ce.gz └── SRR444655.ciri.gz ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── Ularcirc.R ├── Ularcirc_plots.R ├── Ularcirc_standalone.R └── file_io.R ├── inst ├── CITATION ├── extdata │ ├── SRR444655_subset.Chimeric.out.junction.gz │ ├── TwoSzabo.RData │ ├── extdata.txt │ └── extdata_backup.txt └── shiny-app │ └── circRNA │ ├── Global.R │ ├── Server.R │ └── UI.R ├── man ├── BSJ_Fastq_Generate.Rd ├── BSJ_details.Rd ├── BSJ_to_circRNA_sequence.Rd ├── Compatible_Annotation_DBs.Rd ├── FilterChimericJuncs.Rd ├── FilterChimeric_Ularcirc.Rd ├── Junction_Sequence_from_Genome.Rd ├── RAD_score.Rd ├── SelectUniqueJunctions.Rd ├── Ularcirc.Rd ├── chimericFilters.Rd ├── chimericStats.Rd ├── loadSTAR_chimeric.Rd ├── plot_AllJunctions.Rd └── sequence_from_exon_coords.Rd ├── readme.md └── vignettes ├── AnnotatingTwoSzabo.PNG ├── 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