├── CNNpeaks ├── CNNpeaks.png ├── Dockerfile ├── LICENSE ├── LabelManager ├── labelManager.py ├── labelManagerRun.py ├── peakLabelManager.ico ├── run.bat └── setup.py ├── README.md ├── dependencies ├── install_samtools.sh ├── nvidia-docker_install.sh └── samtools-1.8.tar.bz2 ├── geneRef ├── chr1.bed ├── chr10.bed ├── chr11.bed ├── chr12.bed ├── chr13.bed ├── chr14.bed ├── chr15.bed ├── chr16.bed ├── chr17.bed ├── chr18.bed ├── chr19.bed ├── chr2.bed ├── chr20.bed ├── chr21.bed ├── chr22.bed ├── chr3.bed ├── chr4.bed ├── chr5.bed ├── chr6.bed ├── chr7.bed ├── chr8.bed ├── chr9.bed ├── chrX.bed └── chrY.bed ├── install.sh ├── intervalChange.py ├── peakCalling ├── __init__.py ├── bamdepth │ ├── .gitignore │ ├── .gitmodules │ ├── .ipynb_checkpoints │ │ └── read_bam-checkpoint.pyx │ ├── build.sh │ ├── main.c │ ├── read_bam.pyx │ ├── readbam.c │ └── setup.py ├── callPeaks.py ├── genBedRows.pyx ├── readCounts.pyx └── setup.py ├── preProcessing ├── __init__.py └── preProcessing.py ├── scripts ├── .ipynb_checkpoints │ └── makeScore-checkpoint.py ├── filteringPeaks.sh └── makeScore.py ├── setup.py └── utility ├── __init__.py ├── calculateError.py ├── checkData.py ├── errorCall.py ├── labelToBed.py ├── loadLabel.py ├── loadPeak.py ├── randomLabel.py └── utilities.py /CNNpeaks: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/CNNpeaks -------------------------------------------------------------------------------- /CNNpeaks.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/CNNpeaks.png -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/LICENSE -------------------------------------------------------------------------------- /LabelManager/labelManager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/LabelManager/labelManager.py -------------------------------------------------------------------------------- /LabelManager/labelManagerRun.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/LabelManager/labelManagerRun.py -------------------------------------------------------------------------------- /LabelManager/peakLabelManager.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/LabelManager/peakLabelManager.ico -------------------------------------------------------------------------------- /LabelManager/run.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/LabelManager/run.bat -------------------------------------------------------------------------------- /LabelManager/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/LabelManager/setup.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/README.md -------------------------------------------------------------------------------- /dependencies/install_samtools.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/dependencies/install_samtools.sh -------------------------------------------------------------------------------- /dependencies/nvidia-docker_install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/dependencies/nvidia-docker_install.sh -------------------------------------------------------------------------------- /dependencies/samtools-1.8.tar.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/dependencies/samtools-1.8.tar.bz2 -------------------------------------------------------------------------------- /geneRef/chr1.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr1.bed -------------------------------------------------------------------------------- /geneRef/chr10.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr10.bed -------------------------------------------------------------------------------- /geneRef/chr11.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr11.bed -------------------------------------------------------------------------------- /geneRef/chr12.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr12.bed -------------------------------------------------------------------------------- /geneRef/chr13.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr13.bed -------------------------------------------------------------------------------- /geneRef/chr14.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr14.bed -------------------------------------------------------------------------------- /geneRef/chr15.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr15.bed -------------------------------------------------------------------------------- /geneRef/chr16.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr16.bed -------------------------------------------------------------------------------- /geneRef/chr17.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr17.bed -------------------------------------------------------------------------------- /geneRef/chr18.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr18.bed -------------------------------------------------------------------------------- /geneRef/chr19.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr19.bed -------------------------------------------------------------------------------- /geneRef/chr2.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr2.bed -------------------------------------------------------------------------------- /geneRef/chr20.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr20.bed -------------------------------------------------------------------------------- /geneRef/chr21.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr21.bed -------------------------------------------------------------------------------- /geneRef/chr22.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr22.bed -------------------------------------------------------------------------------- /geneRef/chr3.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr3.bed -------------------------------------------------------------------------------- /geneRef/chr4.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr4.bed -------------------------------------------------------------------------------- /geneRef/chr5.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr5.bed -------------------------------------------------------------------------------- /geneRef/chr6.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr6.bed -------------------------------------------------------------------------------- /geneRef/chr7.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr7.bed -------------------------------------------------------------------------------- /geneRef/chr8.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr8.bed -------------------------------------------------------------------------------- /geneRef/chr9.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chr9.bed -------------------------------------------------------------------------------- /geneRef/chrX.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chrX.bed -------------------------------------------------------------------------------- /geneRef/chrY.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/geneRef/chrY.bed -------------------------------------------------------------------------------- /install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/install.sh -------------------------------------------------------------------------------- /intervalChange.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/intervalChange.py -------------------------------------------------------------------------------- /peakCalling/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /peakCalling/bamdepth/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/.gitignore -------------------------------------------------------------------------------- /peakCalling/bamdepth/.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/.gitmodules -------------------------------------------------------------------------------- /peakCalling/bamdepth/.ipynb_checkpoints/read_bam-checkpoint.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/.ipynb_checkpoints/read_bam-checkpoint.pyx -------------------------------------------------------------------------------- /peakCalling/bamdepth/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/build.sh -------------------------------------------------------------------------------- /peakCalling/bamdepth/main.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/main.c -------------------------------------------------------------------------------- /peakCalling/bamdepth/read_bam.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/read_bam.pyx -------------------------------------------------------------------------------- /peakCalling/bamdepth/readbam.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/readbam.c -------------------------------------------------------------------------------- /peakCalling/bamdepth/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/bamdepth/setup.py -------------------------------------------------------------------------------- /peakCalling/callPeaks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/callPeaks.py -------------------------------------------------------------------------------- /peakCalling/genBedRows.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/genBedRows.pyx -------------------------------------------------------------------------------- /peakCalling/readCounts.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/readCounts.pyx -------------------------------------------------------------------------------- /peakCalling/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/peakCalling/setup.py -------------------------------------------------------------------------------- /preProcessing/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /preProcessing/preProcessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/preProcessing/preProcessing.py -------------------------------------------------------------------------------- /scripts/.ipynb_checkpoints/makeScore-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/scripts/.ipynb_checkpoints/makeScore-checkpoint.py -------------------------------------------------------------------------------- /scripts/filteringPeaks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/scripts/filteringPeaks.sh -------------------------------------------------------------------------------- /scripts/makeScore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/scripts/makeScore.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/setup.py -------------------------------------------------------------------------------- /utility/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /utility/calculateError.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/calculateError.py -------------------------------------------------------------------------------- /utility/checkData.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/checkData.py -------------------------------------------------------------------------------- /utility/errorCall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/errorCall.py -------------------------------------------------------------------------------- /utility/labelToBed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/labelToBed.py -------------------------------------------------------------------------------- /utility/loadLabel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/loadLabel.py -------------------------------------------------------------------------------- /utility/loadPeak.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/loadPeak.py -------------------------------------------------------------------------------- /utility/randomLabel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/randomLabel.py -------------------------------------------------------------------------------- /utility/utilities.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/odb9402/CNNPeaks/HEAD/utility/utilities.py --------------------------------------------------------------------------------