MANIFEST.in
requirements.txt
setup.cfg
setup.py
doc/AWS_installation.rst
doc/ChIPseq_modules_HOMER.rst
doc/ChIPseq_modules_MACS.rst
doc/Makefile
doc/RNAseq_Tuxedo_Modules.rst
doc/RNAseq_cancer_modules.rst
doc/RNAseq_cancer_modules_TCGA.rst
doc/RNAseq_counts_modules.rst
doc/RNAseq_counts_modules_TCGA.rst
doc/WGS_WES_modules.rst
doc/about.rst
doc/adding_modules.rst
doc/all_modules.rst
doc/conf.py
doc/contents.rst
doc/copyright.rst
doc/custom_pipelines.rst
doc/databases.rst
doc/dependencies.rst
doc/history.rst
doc/index.rst
doc/installation.rst
doc/make.bat
doc/miRNAseq_Tuxedo_Modules.rst
doc/miRNAseq_counts_modules.rst
doc/mutect_modules.rst
doc/parameter_file.rst
doc/pipelines.rst
doc/requirements.txt
doc/resources.rst
doc/tutorial.rst
doc/omics_pipebuild/doctrees/AWS_installation.doctree
doc/omics_pipebuild/doctrees/ChIPseq_modules_HOMER.doctree
doc/omics_pipebuild/doctrees/ChIPseq_modules_MACS.doctree
doc/omics_pipebuild/doctrees/RNAseq_Tuxedo_Modules.doctree
doc/omics_pipebuild/doctrees/RNAseq_cancer_modules.doctree
doc/omics_pipebuild/doctrees/RNAseq_cancer_modules_TCGA.doctree
doc/omics_pipebuild/doctrees/RNAseq_counts_modules.doctree
doc/omics_pipebuild/doctrees/RNAseq_counts_modules_TCGA.doctree
doc/omics_pipebuild/doctrees/WGS_WES_modules.doctree
doc/omics_pipebuild/doctrees/about.doctree
doc/omics_pipebuild/doctrees/adding_modules.doctree
doc/omics_pipebuild/doctrees/all_modules.doctree
doc/omics_pipebuild/doctrees/contents.doctree
doc/omics_pipebuild/doctrees/copyright.doctree
doc/omics_pipebuild/doctrees/custom_pipelines.doctree
doc/omics_pipebuild/doctrees/databases.doctree
doc/omics_pipebuild/doctrees/dependencies.doctree
doc/omics_pipebuild/doctrees/environment.pickle
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doc/omics_pipebuild/doctrees/index.doctree
doc/omics_pipebuild/doctrees/installation.doctree
doc/omics_pipebuild/doctrees/miRNAseq_Tuxedo_Modules.doctree
doc/omics_pipebuild/doctrees/miRNAseq_counts_modules.doctree
doc/omics_pipebuild/doctrees/mutect_modules.doctree
doc/omics_pipebuild/doctrees/parameter_file.doctree
doc/omics_pipebuild/doctrees/pipelines.doctree
doc/omics_pipebuild/doctrees/resources.doctree
doc/omics_pipebuild/doctrees/tutorial.doctree
doc/omics_pipebuild/html/.buildinfo
doc/omics_pipebuild/html/AWS_installation.html
doc/omics_pipebuild/html/ChIPseq_modules_HOMER.html
doc/omics_pipebuild/html/ChIPseq_modules_MACS.html
doc/omics_pipebuild/html/RNAseq_Tuxedo_Modules.html
doc/omics_pipebuild/html/RNAseq_cancer_modules.html
doc/omics_pipebuild/html/RNAseq_cancer_modules_TCGA.html
doc/omics_pipebuild/html/RNAseq_counts_modules.html
doc/omics_pipebuild/html/RNAseq_counts_modules_TCGA.html
doc/omics_pipebuild/html/WGS_WES_modules.html
doc/omics_pipebuild/html/about.html
doc/omics_pipebuild/html/adding_modules.html
doc/omics_pipebuild/html/all_modules.html
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doc/omics_pipebuild/html/copyright.html
doc/omics_pipebuild/html/custom_pipelines.html
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doc/omics_pipebuild/html/index.html
doc/omics_pipebuild/html/installation.html
doc/omics_pipebuild/html/miRNAseq_Tuxedo_Modules.html
doc/omics_pipebuild/html/miRNAseq_counts_modules.html
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doc/omics_pipebuild/html/searchindex.js
doc/omics_pipebuild/html/tutorial.html
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doc/omics_pipebuild/html/_sources/AWS_installation.txt
doc/omics_pipebuild/html/_sources/ChIPseq_modules_HOMER.txt
doc/omics_pipebuild/html/_sources/ChIPseq_modules_MACS.txt
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doc/omics_pipebuild/html/_sources/RNAseq_cancer_modules.txt
doc/omics_pipebuild/html/_sources/RNAseq_cancer_modules_TCGA.txt
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doc/omics_pipebuild/html/_sources/RNAseq_counts_modules_TCGA.txt
doc/omics_pipebuild/html/_sources/WGS_WES_modules.txt
doc/omics_pipebuild/html/_sources/about.txt
doc/omics_pipebuild/html/_sources/adding_modules.txt
doc/omics_pipebuild/html/_sources/all_modules.txt
doc/omics_pipebuild/html/_sources/contents.txt
doc/omics_pipebuild/html/_sources/copyright.txt
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omics_pipe/ChIPseq.py
omics_pipe/ChIPseq_HOMER.py
omics_pipe/ChIPseq_MACS.py
omics_pipe/RNAseq.py
omics_pipe/RNAseq_DE.py
omics_pipe/RNAseq_TCGA.py
omics_pipe/RNAseq_TCGA_counts.py
omics_pipe/RNAseq_Tuxedo.py
omics_pipe/RNAseq_cancer_report.py
omics_pipe/RNAseq_count_based.py
omics_pipe/SomaticInDels.py
omics_pipe/Tumorseq_MUTECT.py
omics_pipe/WES_GATK.py
omics_pipe/WES_GATK_group_calling.py
omics_pipe/WGS_GATK.py
omics_pipe/WGS_GATK_group_calling.py
omics_pipe/__init__.py
omics_pipe/__version__.py
omics_pipe/cleanup_files.py
omics_pipe/main.py
omics_pipe/miRNAseq.py
omics_pipe/miRNAseq_DE.py
omics_pipe/miRNAseq_count_based.py
omics_pipe/miRNAseq_tuxedo.py
omics_pipe/noveltranscripts.py
omics_pipe/test.py
omics_pipe/utils.py
omics_pipe.egg-info/PKG-INFO
omics_pipe.egg-info/SOURCES.txt
omics_pipe.egg-info/dependency_links.txt
omics_pipe.egg-info/entry_points.txt
omics_pipe.egg-info/requires.txt
omics_pipe.egg-info/top_level.txt
omics_pipe/modules/BreastCancer_RNA_report.py
omics_pipe/modules/ChIP_trim.py
omics_pipe/modules/GATK_preprocessing_WES.py
omics_pipe/modules/GATK_preprocessing_WGS.py
omics_pipe/modules/GATK_variant_discovery.py
omics_pipe/modules/GATK_variant_discovery_group.py
omics_pipe/modules/GATK_variant_filtering.py
omics_pipe/modules/GATK_variant_joint_analysis.py
omics_pipe/modules/RNAseq_QC.py
omics_pipe/modules/RNAseq_report.py
omics_pipe/modules/RNAseq_report_counts.py
omics_pipe/modules/RNAseq_report_tuxedo.py
omics_pipe/modules/TCGA_download.py
omics_pipe/modules/__init__.py
omics_pipe/modules/annotate_peaks.py
omics_pipe/modules/annotate_variants.py
omics_pipe/modules/bowtie.py
omics_pipe/modules/bwa.py
omics_pipe/modules/call_variants.py
omics_pipe/modules/cuffdiff.py
omics_pipe/modules/cuffdiff_miRNA.py
omics_pipe/modules/cufflinks.py
omics_pipe/modules/cufflinks_miRNA.py
omics_pipe/modules/cufflinks_ncRNA.py
omics_pipe/modules/cuffmerge.py
omics_pipe/modules/cuffmerge_miRNA.py
omics_pipe/modules/cuffmergetocompare.py
omics_pipe/modules/cuffmergetocompare_miRNA.py
omics_pipe/modules/custom_R_report.py
omics_pipe/modules/cutadapt_miRNA.py
omics_pipe/modules/fastq_length_filter_miRNA.py
omics_pipe/modules/fastqc.py
omics_pipe/modules/fastqc_miRNA.py
omics_pipe/modules/filter_variants.py
omics_pipe/modules/find_motifs.py
omics_pipe/modules/fusion_catcher.py
omics_pipe/modules/homer_peaks.py
omics_pipe/modules/htseq.py
omics_pipe/modules/htseq_gencode.py
omics_pipe/modules/htseq_miRNA.py
omics_pipe/modules/htseq_ncRNA.py
omics_pipe/modules/intogen.py
omics_pipe/modules/macs.py
omics_pipe/modules/mutect.py
omics_pipe/modules/peak_track.py
omics_pipe/modules/picard_mark_duplicates.py
omics_pipe/modules/read_density.py
omics_pipe/modules/rseqc.py
omics_pipe/modules/snpir_variants.py
omics_pipe/modules/star.py
omics_pipe/modules/star_piRNA.py
omics_pipe/modules/tophat.py
omics_pipe/modules/tophat_miRNA.py
omics_pipe/modules/tophat_ncRNA.py
omics_pipe/parameters/ChIPseq_homer_params.yaml
omics_pipe/parameters/ChIPseq_macs_params.yaml
omics_pipe/parameters/RNAseq_DE_params.yaml
omics_pipe/parameters/RNAseq_cancer_report_params.yaml
omics_pipe/parameters/RNAseq_count_based_params.yaml
omics_pipe/parameters/RNAseq_params.yaml
omics_pipe/parameters/RNAseq_tuxedo_params.yaml
omics_pipe/parameters/Tumorseq_mutect_params.yaml
omics_pipe/parameters/WES_GATK_parameters.yaml
omics_pipe/parameters/WGS_GATK_params.yaml
omics_pipe/parameters/__init__.py
omics_pipe/parameters/default_parameters.py
omics_pipe/parameters/miRNA_params.yaml
omics_pipe/parameters/miRNAseq_count_based_params.yaml
omics_pipe/parameters/miRNAseq_tuxedo_params.yaml
omics_pipe/parameters/noveltranscripts_params.py
omics_pipe/scripts/BreastCancer_RNA_report.sh
omics_pipe/scripts/ChIP_trim_PE.sh
omics_pipe/scripts/ChIP_trim_SE.sh
omics_pipe/scripts/GATK_genotypeGVCFs_3.2-2.sh
omics_pipe/scripts/GATK_preprocessing_WES_2.8-1.sh
omics_pipe/scripts/GATK_preprocessing_WES_3.2-2.sh
omics_pipe/scripts/GATK_preprocessing_WGS_2.8-1.sh
omics_pipe/scripts/GATK_variant_discovery_2.8-1.sh
omics_pipe/scripts/GATK_variant_discovery_3.2-2.sh
omics_pipe/scripts/GATK_variant_discovery_group_3.2-2.sh
omics_pipe/scripts/GATK_variant_filtering_2.8-1.sh
omics_pipe/scripts/GATK_variant_filtering_3.2-2.sh
omics_pipe/scripts/GATK_variant_filtering_group_3.2-2.sh
omics_pipe/scripts/RNAseq_QC.sh
omics_pipe/scripts/RNAseq_counts.Rmd
omics_pipe/scripts/RNAseq_report_counts.sh
omics_pipe/scripts/RNAseq_report_tuxedo.sh
omics_pipe/scripts/TCGA_download.sh
omics_pipe/scripts/__init__.py
omics_pipe/scripts/annotate_peaks.sh
omics_pipe/scripts/bowtie_drmaa_PE.sh
omics_pipe/scripts/bowtie_drmaa_SE.sh
omics_pipe/scripts/bwa_drmaa_PE_DNA.sh
omics_pipe/scripts/bwa_drmaa_RNA.sh
omics_pipe/scripts/bwa_drmaa_SE_DNA.sh
omics_pipe/scripts/bwa_snpir_drmaa.sh
omics_pipe/scripts/cleanup.sh
omics_pipe/scripts/config.pm
omics_pipe/scripts/cuffdiff_drmaa.sh
omics_pipe/scripts/cufflinks_drmaa.sh
omics_pipe/scripts/cuffmerge_drmaa.sh
omics_pipe/scripts/cuffmergetocompare_drmaa.sh
omics_pipe/scripts/custom_R_report.sh
omics_pipe/scripts/cutadapt_drmaa.sh
omics_pipe/scripts/extractvcf.R
omics_pipe/scripts/fastq_length_filter.py
omics_pipe/scripts/fastqc_drmaa.sh
omics_pipe/scripts/filter_snpir_drmaa.sh
omics_pipe/scripts/find_motifs.sh
omics_pipe/scripts/fusion_catcher_drmaa.sh
omics_pipe/scripts/homer_peaks.sh
omics_pipe/scripts/htseq_drmaa.sh
omics_pipe/scripts/intogen_config.sh
omics_pipe/scripts/intogen_config_AWS.sh
omics_pipe/scripts/intogen_drmaa.sh
omics_pipe/scripts/knitMeR_RNA_counts.R
omics_pipe/scripts/macs_drmaa.sh
omics_pipe/scripts/mutect.sh
omics_pipe/scripts/peak_track.sh
omics_pipe/scripts/picard_mark_duplicates.sh
omics_pipe/scripts/read_density.sh
omics_pipe/scripts/removeLines.R
omics_pipe/scripts/rseqc_drmaa.sh
omics_pipe/scripts/run_py.sh
omics_pipe/scripts/run_py_script.sh
omics_pipe/scripts/snpEff.config
omics_pipe/scripts/snpir_drmaa.sh
omics_pipe/scripts/star_drmaa_PE.sh
omics_pipe/scripts/star_drmaa_SE.sh
omics_pipe/scripts/tophat_drmaa_PE.sh
omics_pipe/scripts/tophat_drmaa_SE.sh
omics_pipe/scripts/tophat_drmaa_SE_ncrna.sh
omics_pipe/scripts/tophat_drmaa_miRNA.sh
omics_pipe/scripts/tophat_drmaa_ncrna.sh
omics_pipe/scripts/unBzip.sh
omics_pipe/scripts/unGzip.sh
omics_pipe/scripts/varannotate_drmaa_bash.sh
omics_pipe/scripts/varcall_drmaa_bash.sh
omics_pipe/scripts/SNPiR/config.pm
omics_pipe/scripts/reporting/__init__.py
omics_pipe/scripts/reporting/oncorep.md
omics_pipe/scripts/reporting/figure/BiocartaPlots.png
omics_pipe/scripts/reporting/figure/BiocartaPlots1.png
omics_pipe/scripts/reporting/figure/BiocartaPlots10.png
omics_pipe/scripts/reporting/figure/BiocartaPlots11.png
omics_pipe/scripts/reporting/figure/BiocartaPlots12.png
omics_pipe/scripts/reporting/figure/BiocartaPlots13.png
omics_pipe/scripts/reporting/figure/BiocartaPlots14.png
omics_pipe/scripts/reporting/figure/BiocartaPlots15.png
omics_pipe/scripts/reporting/figure/BiocartaPlots16.png
omics_pipe/scripts/reporting/figure/BiocartaPlots17.png
omics_pipe/scripts/reporting/figure/BiocartaPlots18.png
omics_pipe/scripts/reporting/figure/BiocartaPlots19.png
omics_pipe/scripts/reporting/figure/BiocartaPlots2.png
omics_pipe/scripts/reporting/figure/BiocartaPlots3.png
omics_pipe/scripts/reporting/figure/BiocartaPlots4.png
omics_pipe/scripts/reporting/figure/BiocartaPlots5.png
omics_pipe/scripts/reporting/figure/BiocartaPlots6.png
omics_pipe/scripts/reporting/figure/BiocartaPlots7.png
omics_pipe/scripts/reporting/figure/BiocartaPlots8.png
omics_pipe/scripts/reporting/figure/BiocartaPlots9.png
omics_pipe/scripts/reporting/figure/NCIPlots.png
omics_pipe/scripts/reporting/figure/NCIPlots1.png
omics_pipe/scripts/reporting/figure/NCIPlots10.png
omics_pipe/scripts/reporting/figure/NCIPlots11.png
omics_pipe/scripts/reporting/figure/NCIPlots12.png
omics_pipe/scripts/reporting/figure/NCIPlots13.png
omics_pipe/scripts/reporting/figure/NCIPlots14.png
omics_pipe/scripts/reporting/figure/NCIPlots15.png
omics_pipe/scripts/reporting/figure/NCIPlots16.png
omics_pipe/scripts/reporting/figure/NCIPlots17.png
omics_pipe/scripts/reporting/figure/NCIPlots18.png
omics_pipe/scripts/reporting/figure/NCIPlots2.png
omics_pipe/scripts/reporting/figure/NCIPlots3.png
omics_pipe/scripts/reporting/figure/NCIPlots4.png
omics_pipe/scripts/reporting/figure/NCIPlots5.png
omics_pipe/scripts/reporting/figure/NCIPlots6.png
omics_pipe/scripts/reporting/figure/NCIPlots7.png
omics_pipe/scripts/reporting/figure/NCIPlots8.png
omics_pipe/scripts/reporting/figure/NCIPlots9.png
omics_pipe/scripts/reporting/figure/ReactomePlots1.png
omics_pipe/scripts/reporting/figure/ReactomePlots10.png
omics_pipe/scripts/reporting/figure/ReactomePlots11.png
omics_pipe/scripts/reporting/figure/ReactomePlots12.png
omics_pipe/scripts/reporting/figure/ReactomePlots13.png
omics_pipe/scripts/reporting/figure/ReactomePlots14.png
omics_pipe/scripts/reporting/figure/ReactomePlots15.png
omics_pipe/scripts/reporting/figure/ReactomePlots16.png
omics_pipe/scripts/reporting/figure/ReactomePlots17.png
omics_pipe/scripts/reporting/figure/ReactomePlots18.png
omics_pipe/scripts/reporting/figure/ReactomePlots19.png
omics_pipe/scripts/reporting/figure/ReactomePlots2.png
omics_pipe/scripts/reporting/figure/ReactomePlots20.png
omics_pipe/scripts/reporting/figure/ReactomePlots21.png
omics_pipe/scripts/reporting/figure/ReactomePlots22.png
omics_pipe/scripts/reporting/figure/ReactomePlots23.png
omics_pipe/scripts/reporting/figure/ReactomePlots24.png
omics_pipe/scripts/reporting/figure/ReactomePlots25.png
omics_pipe/scripts/reporting/figure/ReactomePlots26.png
omics_pipe/scripts/reporting/figure/ReactomePlots27.png
omics_pipe/scripts/reporting/figure/ReactomePlots28.png
omics_pipe/scripts/reporting/figure/ReactomePlots29.png
omics_pipe/scripts/reporting/figure/ReactomePlots3.png
omics_pipe/scripts/reporting/figure/ReactomePlots30.png
omics_pipe/scripts/reporting/figure/ReactomePlots31.png
omics_pipe/scripts/reporting/figure/ReactomePlots32.png
omics_pipe/scripts/reporting/figure/ReactomePlots33.png
omics_pipe/scripts/reporting/figure/ReactomePlots34.png
omics_pipe/scripts/reporting/figure/ReactomePlots35.png
omics_pipe/scripts/reporting/figure/ReactomePlots36.png
omics_pipe/scripts/reporting/figure/ReactomePlots37.png
omics_pipe/scripts/reporting/figure/ReactomePlots38.png
omics_pipe/scripts/reporting/figure/ReactomePlots39.png
omics_pipe/scripts/reporting/figure/ReactomePlots4.png
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omics_pipe/scripts/reporting/figure/reliableGEPDensityPlot.png
omics_pipe/scripts/reporting/src/RNAseq_counts.Rmd
omics_pipe/scripts/reporting/src/RNAseq_tuxedo.Rmd
omics_pipe/scripts/reporting/src/__init__.py
omics_pipe/scripts/reporting/src/custom.css
omics_pipe/scripts/reporting/src/knitMeR.R
omics_pipe/scripts/reporting/src/oncorep.Rmd
omics_pipe/scripts/reporting/src/core/__init__.py
omics_pipe/scripts/reporting/src/core/dataIn.R
omics_pipe/scripts/reporting/src/core/functions.R
omics_pipe/scripts/reporting/src/core/gene_table.R
omics_pipe/scripts/reporting/src/core/setup.R
omics_pipe/scripts/reporting/src/modules/KEGGParse.R
omics_pipe/scripts/reporting/src/modules/PW_tables_and_viz.R
omics_pipe/scripts/reporting/src/modules/RNAseq_tuxedo.Rmd
omics_pipe/scripts/reporting/src/modules/__init__.py
omics_pipe/scripts/reporting/src/modules/brca_mol_class.R
omics_pipe/scripts/reporting/src/modules/diff_exp.R
omics_pipe/scripts/reporting/src/modules/dog.R
omics_pipe/scripts/reporting/src/modules/dps.R
omics_pipe/scripts/reporting/src/modules/fusion_catcher.R
omics_pipe/scripts/reporting/src/modules/intogen.R
omics_pipe/scripts/reporting/src/modules/qual_ctrl.R
omics_pipe/scripts/reporting/src/modules/reliable_gep.R
omics_pipe/scripts/reporting/src/modules/snpAnnotation.R
omics_pipe/scripts/reporting/src/modules/spia.R
tests/ChIP_test1_chip.fastq
tests/ChIP_test1_input.fastq
tests/ChIP_test2_chip.fastq
tests/ChIP_test2_input.fastq
tests/__init__.py
tests/custom.py
tests/custom_TCGA_counts.py
tests/custom_TCGA_counts2.py
tests/main_test.py
tests/main_test2.py
tests/run_test.sh
tests/test1.fastq
tests/test2.fastq
tests/test3.fastq
tests/test_DNA1.fastq
tests/test_DNA1_1.fastq
tests/test_DNA1_2.fastq
tests/test_DNA2.fastq
tests/test_DNA2_1.fastq
tests/test_DNA2_2.fastq
tests/test_RNA1_1.fastq
tests/test_RNA1_2.fastq
tests/test_RNA2_1.fastq
tests/test_RNA2_2.fastq
tests/test_params.yaml
tests/test_params_ChIPseq_HOMER.yaml
tests/test_params_ChIPseq_HOMER_AWS.yaml
tests/test_params_ChIPseq_MACS.yaml
tests/test_params_RNAseq_TCGA.yaml
tests/test_params_RNAseq_TCGA_counts.yaml
tests/test_params_RNAseq_Tuxedo.yaml
tests/test_params_RNAseq_Tuxedo_AWS.yaml
tests/test_params_RNAseq_cancer.yaml
tests/test_params_RNAseq_counts.yaml
tests/test_params_RNAseq_counts_AWS.yaml
tests/test_params_WES_GATK.yaml
tests/test_params_WES_GATK_AWS.yaml
tests/test_params_WES_GATK_group_calling.yaml
tests/test_params_WGS_GATK.yaml
tests/test_params_miRNAseq_Tuxedo.yaml
tests/test_params_miRNAseq_counts.yaml
tests/test_params_test.yaml