Authors.rst
MANIFEST.in
NEWS
README.md
setup.cfg
setup.py
bap/.DS_Store
bap/__init__.py
bap/__init__.pyc
bap/bap1ProjectClass.py
bap/bap2ProjectClass.py
bap/bapFragProjectClass.py
bap/bapHelp.py
bap/cli.pyc
bap/cli_bap2.py
bap/cli_bap_bulk_frag.py
bap/cli_bap_frag.py
bap/cli_old_dontEdit.py
bap/cli_reanno.py
bap/__pycache__/.DS_Store
bap/__pycache__/__init__.cpython-36.pyc
bap/__pycache__/annoall.cpython-36.pyc
bap/__pycache__/bap1ProjectClass.cpython-36.pyc
bap/__pycache__/bap2ProjectClass.cpython-36.pyc
bap/__pycache__/bapFragProjectClass.cpython-36.pyc
bap/__pycache__/bapHelp.cpython-36.pyc
bap/__pycache__/bapProjectClass.cpython-36.pyc
bap/__pycache__/cli.cpython-36.pyc
bap/__pycache__/cli_bap2.cpython-36.pyc
bap/__pycache__/cli_bap_bulk_frag.cpython-36.pyc
bap/__pycache__/cli_bap_frag.cpython-36.pyc
bap/__pycache__/cli_old_dontEdit.cpython-36.pyc
bap/__pycache__/cli_reanno.cpython-36.pyc
bap/anno/.DS_Store
bap/anno/TSS/.DS_Store
bap/anno/TSS/GRCh37.refGene.TSS.bed
bap/anno/TSS/GRCh38.refGene.TSS.bed
bap/anno/TSS/GRCm37.refGene.TSS.bed
bap/anno/TSS/GRCm38.refGene.TSS.bed
bap/anno/TSS/hg19-mm10.refGene.TSS.bed
bap/anno/TSS/hg19-mm10_nochr.refGene.TSS.bed
bap/anno/TSS/hg19.refGene.TSS.bed
bap/anno/TSS/hg19_mm10_c.refGene.TSS.bed
bap/anno/TSS/hg38.refGene.TSS.bed
bap/anno/TSS/mm10.refGene.TSS.bed
bap/anno/TSS/mm9.refGene.TSS.bed
bap/anno/bedtools/chrom_GRCh37.sizes
bap/anno/bedtools/chrom_GRCh38.sizes
bap/anno/bedtools/chrom_GRCm37.sizes
bap/anno/bedtools/chrom_GRCm38.sizes
bap/anno/bedtools/chrom_hg19-mm10.sizes
bap/anno/bedtools/chrom_hg19-mm10_nochr.sizes
bap/anno/bedtools/chrom_hg19.sizes
bap/anno/bedtools/chrom_hg19_mm10_c.sizes
bap/anno/bedtools/chrom_hg38.sizes
bap/anno/bedtools/chrom_mm10.sizes
bap/anno/bedtools/chrom_mm9.sizes
bap/anno/blacklist/GRCh37.full.blacklist.bed
bap/anno/blacklist/GRCh38.full.blacklist.bed
bap/anno/blacklist/GRCm37.full.blacklist.bed
bap/anno/blacklist/GRCm38.full.blacklist.bed
bap/anno/blacklist/hg19-mm10.full.blacklist.bed
bap/anno/blacklist/hg19-mm10_nochr.full.blacklist.bed
bap/anno/blacklist/hg19.full.blacklist.bed
bap/anno/blacklist/hg19_mm10_c.full.blacklist.bed
bap/anno/blacklist/hg38.full.blacklist.bed
bap/anno/blacklist/mm10.full.blacklist.bed
bap/anno/blacklist/mm9.full.blacklist.bed
bap/barcode/.DS_Store
bap/barcode/cli_barcode.py
bap/barcode/__pycache__/cli_barcode.cpython-36.pyc
bap/barcode/modes/.DS_Store
bap/barcode/modes/barcodeHelp.py
bap/barcode/modes/biorad_v1.py
bap/barcode/modes/biorad_v2-multi.py
bap/barcode/modes/biorad_v2.py
bap/barcode/modes/__pycache__/barcodeHelp.cpython-36.pyc
bap/bin/.DS_Store
bap/bin/R/.DS_Store
bap/bin/R/00_knee_CL.R
bap/bin/R/10b_knee_execute.R
bap/bin/R/11a_computeNCperRead.R
bap/bin/R/12_fragOverlapMetricsChr.R
bap/bin/R/13_callDoublets.R
bap/bin/R/15_ncReadCleanup.R
bap/bin/R/16_qualityControlReport_SE.R
bap/bin/R/19_makeKneePlots.R
bap/bin/R/21_annotate_fragments.R
bap/bin/R/21a_annotate_fragments_bap2_frags.R
bap/bin/R/21b_processRawFragments_bap_frag_bulk.R
bap/bin/R/22_fragOverlapMetricsChr_bap2.R
bap/bin/R/23_callDoublets_bap2.R
bap/bin/R/24_reannoFrags_bap2.R
bap/bin/R/26a_QCsimple_bap2.R
bap/bin/R/26b_QCadvanced_SE_bap2.R
bap/bin/R/zzz_fragOverlapMetricsBinChr_bap2.R
bap/bin/python/.DS_Store
bap/bin/python/10_quantBarcode_Filt.py
bap/bin/python/11b_annoFiltNC.py
bap/bin/python/14_paintDropBarcode.py
bap/bin/python/17_processMito.py
bap/bin/python/20_names_split_filt.py
bap/bin/python/20a_nonames_split_filt.py
bap/bin/python/25_paintDropBarcode_bap2.py
bap/bin/snake/.DS_Store
bap/bin/snake/Snakefile.bap.chr
bap/bin/snake/Snakefile.bap2.chr
bap/bin/snake/Snakefile.bap_bulk_frags
bap/bin/snake/Snakefile.bap_frags
bap_atac.egg-info/PKG-INFO
bap_atac.egg-info/SOURCES.txt
bap_atac.egg-info/dependency_links.txt
bap_atac.egg-info/entry_points.txt
bap_atac.egg-info/not-zip-safe
bap_atac.egg-info/requires.txt
bap_atac.egg-info/top_level.txt