.gitignore_global
README.md
setup.cfg
setup.py
clipper/__init__.py
clipper/gtf2bed.sh
clipper.egg-info/PKG-INFO
clipper.egg-info/SOURCES.txt
clipper.egg-info/dependency_links.txt
clipper.egg-info/entry_points.txt
clipper.egg-info/requires.txt
clipper.egg-info/top_level.txt
clipper/data/__init__.py
clipper/data/ce10.AS.STRUCTURE.COMPILED.gff
clipper/data/ce10.AS.STRUCTURE.COMPILED.gff2
clipper/data/dm3.AS.STRUCTURE.COMPILED.gff
clipper/data/hg19.AS.STRUCTURE.COMPILED.gff
clipper/data/mm10.AS.STRUCTURE.COMPILED.gff
clipper/data/mm9.AS.STRUCTURE.COMPILED.gff
clipper/data/test.AS.STRUCTURE_genes.BED.gz
clipper/data/test.AS.STRUCTURE_mRNA.lengths
clipper/data/test.AS.STRUCTURE_premRNA.lengths
clipper/data/regions/__init__.py
clipper/data/regions/ce10_cds.bed
clipper/data/regions/ce10_distintron500.bed
clipper/data/regions/ce10_exons.bed
clipper/data/regions/ce10_exons.mrg.bed
clipper/data/regions/ce10_five_prime_ends.bed
clipper/data/regions/ce10_five_prime_utrs.bed
clipper/data/regions/ce10_genes.bed
clipper/data/regions/ce10_introns.bed
clipper/data/regions/ce10_poly_a_sites.bed
clipper/data/regions/ce10_proxintron500.bed
clipper/data/regions/ce10_start_codons.bed
clipper/data/regions/ce10_stop_codons.bed
clipper/data/regions/ce10_three_prime_ends.bed
clipper/data/regions/ce10_three_prime_utrs.bed
clipper/data/regions/ce10_transcription_start_sites.bed
clipper/data/regions/hg19_cds.bed
clipper/data/regions/hg19_distintron500.bed
clipper/data/regions/hg19_exons.bed
clipper/data/regions/hg19_five_prime_ends.bed
clipper/data/regions/hg19_five_prime_utrs.bed
clipper/data/regions/hg19_genes.bed
clipper/data/regions/hg19_introns.bed
clipper/data/regions/hg19_poly_a_sites.bed
clipper/data/regions/hg19_proxintron500.bed
clipper/data/regions/hg19_start_codons.bed
clipper/data/regions/hg19_stop_codons.bed
clipper/data/regions/hg19_three_prime_ends.bed
clipper/data/regions/hg19_three_prime_utrs.bed
clipper/data/regions/hg19_transcription_start_sites.bed
clipper/data/regions/mm9_cds.bed
clipper/data/regions/mm9_distintron500.bed
clipper/data/regions/mm9_exons.bed
clipper/data/regions/mm9_five_prime_utrs.bed
clipper/data/regions/mm9_proxintron500.bed
clipper/data/regions/mm9_three_prime_utrs.bed
clipper/src/AS_Structure_tools.py
clipper/src/CLIP_analysis.py
clipper/src/CLIP_analysis_display.py
clipper/src/__init__.py
clipper/src/call_peak.py
clipper/src/get_ce10_genomic_regions.py
clipper/src/get_genomic_regions.py
clipper/src/kmerdiff.py
clipper/src/peakfinder.py
clipper/src/peaksmodule.cc
clipper/src/readsToWiggle.c
clipper/src/readsToWiggle.pyx
clipper/test/__init__.py
clipper/test/test_CLIP_Analysis_Display.py
clipper/test/test_CLIP_analysis.py
clipper/test/test_call_peak.py
clipper/test/test_classic.py
clipper/test/test_kmerdiff.py
clipper/test/test_peakfinder.py
clipper/test/test_peaks.py
clipper/test/test_spline.py
clipper/test/data/CLIP_Analysis_test.bed
clipper/test/data/FOX2Brain-05.15.09.polyATrim.adapterTrim.rmRep.sorted.rmDup.peaks.bed
clipper/test/data/allup_test.bam
clipper/test/data/allup_test.bam.bai
clipper/test/data/allup_test.neg.bw
clipper/test/data/allup_test.pos.bw
clipper/test/data/allup_test.rmdup.bam
clipper/test/data/clip_analysis_test_peak_results.bed
clipper/test/data/clip_analysis_test_peak_results.bed.exon.rand.0.BED
clipper/test/data/clip_analysis_test_peak_results.bed.exon.real.BED
clipper/test/data/compseq_test.fasta
clipper/test/data/compseq_test.out
clipper/test/data/compseq_test_2.fasta
clipper/test/data/data.gtf
clipper/test/data/data_2.gtf
clipper/test/data/ensembl_test.gtf
clipper/test/data/foo
clipper/test/data/hg19_genes.bed
clipper/test/data/indexed_test.bam
clipper/test/data/motif_distance_test_cluster.bed
clipper/test/data/motif_distance_test_motif.bed
clipper/test/data/not_indexed_test.bam
clipper/test/data/peak_results.BED
clipper/test/data/peak_results_no_overlap.BED
clipper/test/data/rmdup_test.bam
clipper/test/data/test.gtf
clipper/test/data/test.tx.1.AS.STRUCTURE
clipper/test/data/test_bed_creation.bed
clipper/test/data/test_peakfinder.py
clipper/test/data/transcriptome_cutoff.bam
clipper/test/data/transcriptome_filter.sort.bam
clipper/test/data/test/clip_analysis_test_peak_results.bed.all.random.fa
clipper/test/data/test/clip_analysis_test_peak_results.bed.all.real.fa