├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── INSTALL ├── THANKS ├── data_structure.json ├── manual.md ├── releases.md └── supplementary.md ├── rseqc ├── __init__.py ├── modules │ ├── FPKM_count.py │ ├── RNA_fragment_size.py │ ├── RPKM_saturation.py │ ├── __init__.py │ ├── bam2fq.py │ ├── bam2wig.py │ ├── bam_stats.py │ ├── clipping_profile.py │ ├── deletion_profile.py │ ├── divide_bam.py │ ├── geneBody_coverage.py │ ├── geneBody_coverage2.py │ ├── infer_experiment.py │ ├── inner_distance.py │ ├── insertion_profile.py │ ├── junction_annotation.py │ ├── junction_saturation.py │ ├── mismatch_profile.py │ ├── normalize_bigwig.py │ ├── overlay_bigwig.py │ ├── read_GC.py │ ├── read_NVC.py │ ├── read_dist.py │ ├── read_duplication.py │ ├── read_hexamer.py │ ├── read_quality.py │ ├── split_bam.py │ ├── split_paired_bam.py │ └── tin.py ├── parsers │ ├── BED.py │ ├── BedWrapper.py │ ├── GTF.py │ └── __init__.py └── qcmodule │ ├── BED.py │ ├── FrameKmer.py │ ├── PSL.py │ ├── SAM.py │ ├── __init__.py │ ├── annoGene.py │ ├── bam_cigar.py │ ├── changePoint.py │ ├── cigar.py │ ├── dotProduct.py │ ├── fasta.py │ ├── fastq.py │ ├── fickett.py │ ├── getBamFiles.py │ ├── mystat.py │ ├── orf.py │ ├── poisson.py │ ├── quantile.py │ ├── twoList.py │ └── wiggle.py ├── scripts └── rseqc ├── setup.cfg ├── setup.py └── src ├── binBits.c ├── binBits.h ├── bunzip ├── micro-bunzip.c └── micro-bunzip.h ├── cluster.c ├── cluster.h ├── kent ├── bits.c ├── bits.h ├── common.c └── common.h ├── pwm_utils.c ├── pwm_utils.h └── samtools ├── bgzf.c ├── bgzf.h └── khash.h /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashBioinformaticsPlatform/RSeQC/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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