CHANGES.txt
LICENSE.txt
MANIFEST.in
README.md
README.rst
requirements.txt
setup.cfg
setup.py
bin/bamCompare
bin/bamCoverage
bin/bamPEFragmentSize
bin/bigwigCompare
bin/computeGCBias
bin/computeMatrix
bin/computeMatrixOperations
bin/correctGCBias
bin/deeptools
bin/estimateScaleFactor
bin/multiBamSummary
bin/multiBigwigSummary
bin/plotCorrelation
bin/plotCoverage
bin/plotEnrichment
bin/plotFingerprint
bin/plotHeatmap
bin/plotPCA
bin/plotProfile
deeptools/SES_scaleFactor.py
deeptools/__init__.py
deeptools/_version.py
deeptools/bamCompare.py
deeptools/bamCoverage.py
deeptools/bamHandler.py
deeptools/bamPEFragmentSize.py
deeptools/bigwigCompare.py
deeptools/computeGCBias.py
deeptools/computeMatrix.py
deeptools/computeMatrixOperations.py
deeptools/correctGCBias.py
deeptools/correctReadCounts.py
deeptools/correlation.py
deeptools/correlation_heatmap.py
deeptools/countReadsPerBin.py
deeptools/deepBlue.py
deeptools/deeptools_list_tools.py
deeptools/getFragmentAndReadSize.py
deeptools/getRatio.py
deeptools/getScaleFactor.py
deeptools/getScorePerBigWigBin.py
deeptools/heatmapper.py
deeptools/heatmapper_utilities.py
deeptools/mapReduce.py
deeptools/multiBamSummary.py
deeptools/multiBigwigSummary.py
deeptools/parserCommon.py
deeptools/plotCorrelation.py
deeptools/plotCoverage.py
deeptools/plotEnrichment.py
deeptools/plotFingerprint.py
deeptools/plotHeatmap.py
deeptools/plotPCA.py
deeptools/plotProfile.py
deeptools/sumCoveragePerBin.py
deeptools/utilities.py
deeptools/writeBedGraph.py
deeptools/writeBedGraph_bam_and_bw.py
deeptools/config/__init__.py
deeptools/config/deeptools.cfg
deeptools/test/__init__.py
deeptools/test/test_bamCoverage_and_bamCompare.py
deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py
deeptools/test/test_computeMatrixOperations.py
deeptools/test/test_countReadsPerBin.py
deeptools/test/test_heatmapper.py
deeptools/test/test_multiBamSummary.py
deeptools/test/test_plotCoverage.py
deeptools/test/test_tools.py
deeptools/test/test_writeBedGraph.py
deeptools/test/test_corrGC/R_gc
deeptools/test/test_corrGC/R_gc_paired.txt
deeptools/test/test_corrGC/extra_sampling.bed
deeptools/test/test_corrGC/filter_out.bed
deeptools/test/test_corrGC/frequencies_data.txt
deeptools/test/test_corrGC/mappability.bg
deeptools/test/test_corrGC/mappability.bw
deeptools/test/test_corrGC/paired.bam
deeptools/test/test_corrGC/paired.bam.bai
deeptools/test/test_corrGC/sequence.2bit
deeptools/test/test_corrGC/sequence.fa
deeptools/test/test_corrGC/sequence.fa.fai
deeptools/test/test_corrGC/sizes
deeptools/test/test_corrGC/test.bam
deeptools/test/test_corrGC/test.bam.bai
deeptools/test/test_corrGC/test.sam
deeptools/test/test_corrGC/test_paired.bam
deeptools/test/test_corrGC/test_paired.bam.bai
deeptools/test/test_corrGC/test_paired.sam
deeptools/test/test_data/computeMatrixOperations.bed
deeptools/test/test_data/computeMatrixOperations.mat.gz
deeptools/test/test_data/make_test_data.sh
deeptools/test/test_data/test.bed3
deeptools/test/test_data/test.gtf
deeptools/test/test_data/test1.bam
deeptools/test/test_data/test1.bam.bai
deeptools/test/test_data/test1.bg
deeptools/test/test_data/test1.bw.bw
deeptools/test/test_data/test1.sam
deeptools/test/test_data/test2.bam
deeptools/test/test_data/test2.bam.bai
deeptools/test/test_data/test2.bg
deeptools/test/test_data/test2.sam
deeptools/test/test_data/testA.bam
deeptools/test/test_data/testA.bam.bai
deeptools/test/test_data/testA.bw
deeptools/test/test_data/testA.sam
deeptools/test/test_data/testA_offset-1.bw
deeptools/test/test_data/testA_offset1.bw
deeptools/test/test_data/testA_offset1_10.bw
deeptools/test/test_data/testA_offset20_-4.bw
deeptools/test/test_data/testA_skipNAs.bw
deeptools/test/test_data/testB.bam
deeptools/test/test_data/testB.bam.bai
deeptools/test/test_data/testB.bw
deeptools/test/test_data/testB.sam
deeptools/test/test_data/testB_skipNAs.bw
deeptools/test/test_data/test_filtering.bam
deeptools/test/test_data/test_filtering.bam.bai
deeptools/test/test_data/test_filtering.blacklist.bed
deeptools/test/test_data/test_filtering2.bam
deeptools/test/test_data/test_filtering2.bam.bai
deeptools/test/test_data/test_paired.bam
deeptools/test/test_data/test_paired.bam.bai
deeptools/test/test_data/test_paired.sam
deeptools/test/test_data/test_paired2.bam
deeptools/test/test_data/test_paired2.bam.bai
deeptools/test/test_data/test_paired2.bw
deeptools/test/test_data/test_paired2.sam
deeptools/test/test_data/test_proper_pair_filtering.bam
deeptools/test/test_data/test_proper_pair_filtering.bam.bai
deeptools/test/test_heatmapper/#test.bg#
deeptools/test/test_heatmapper/group1.bed
deeptools/test/test_heatmapper/group2.bed
deeptools/test/test_heatmapper/heatmap_master_multi_color.svg
deeptools/test/test_heatmapper/heatmap_master_multi_colormap_no_box.svg
deeptools/test/test_heatmapper/heatmap_master_multi_pergroup.svg
deeptools/test/test_heatmapper/make_test_data.sh
deeptools/test/test_heatmapper/master.mat
deeptools/test/test_heatmapper/master.mat.gz
deeptools/test/test_heatmapper/master.svg
deeptools/test/test_heatmapper/master.tab
deeptools/test/test_heatmapper/master_TES.mat
deeptools/test/test_heatmapper/master_center.mat
deeptools/test/test_heatmapper/master_extend_beyond_chr_size.mat
deeptools/test/test_heatmapper/master_gtf.mat
deeptools/test/test_heatmapper/master_metagene.mat
deeptools/test/test_heatmapper/master_multi.mat
deeptools/test/test_heatmapper/master_multi.mat.gz
deeptools/test/test_heatmapper/master_multibed.mat
deeptools/test/test_heatmapper/master_nan_to_zero.mat
deeptools/test/test_heatmapper/master_relabeled.svg
deeptools/test/test_heatmapper/master_scale_reg.mat
deeptools/test/test_heatmapper/master_scale_reg.mat.gz
deeptools/test/test_heatmapper/master_scale_reg.svg
deeptools/test/test_heatmapper/master_unscaled.mat
deeptools/test/test_heatmapper/out.bed
deeptools/test/test_heatmapper/profile_master.png
deeptools/test/test_heatmapper/profile_master.svg
deeptools/test/test_heatmapper/profile_master_heatmap.svg
deeptools/test/test_heatmapper/profile_master_multi.svg
deeptools/test/test_heatmapper/profile_master_multi_pergroup.svg
deeptools/test/test_heatmapper/profile_master_overlap_lines.svg
deeptools/test/test_heatmapper/test.bed
deeptools/test/test_heatmapper/test.bg
deeptools/test/test_heatmapper/test.bw
deeptools/test/test_heatmapper/test.sizes
deeptools/test/test_heatmapper/test2.bed
deeptools/test/test_heatmapper/unscaled.bed
deeptools/test/test_heatmapper/unscaled.bigWig
deeptools/test/test_plotCoverage/make_test_files.sh
deeptools/test/test_plotCoverage/outRawCounts_default.tabular
deeptools/test/test_plotCoverage/plotCoverage_default.svg
deeptoolsintervals/__init__.py
deeptoolsintervals/enrichment.py
deeptoolsintervals/parse.py
deeptoolsintervals/test/GRCh38.84.2.gtf.gz
deeptoolsintervals/test/GRCh38.84.bed
deeptoolsintervals/test/GRCh38.84.bed12.bz2
deeptoolsintervals/test/GRCh38.84.bed2
deeptoolsintervals/test/GRCh38.84.bed6
deeptoolsintervals/test/GRCh38.84.gtf.gz
deeptoolsintervals/test/GRCh38.84.labels.bed
deeptoolsintervals/test/noOverlaps.bed
deeptoolsintervals/tree/findOverlaps.c
deeptoolsintervals/tree/gtf.c
deeptoolsintervals/tree/gtf.h
deeptoolsintervals/tree/hashTable.c
deeptoolsintervals/tree/kseq.h
deeptoolsintervals/tree/kstring.h
deeptoolsintervals/tree/murmur3.c
deeptoolsintervals/tree/murmur3.h
deeptoolsintervals/tree/tree.c
deeptoolsintervals/tree/tree.h
scripts/mappabilityBigWig_to_unmappableBed.sh
scripts/split_bed_into_multiple_files.py