├── .DS_Store ├── LICENSE ├── README.md ├── cgc ├── Mapping_file_lucky_50.txt ├── Mapping_file_lucky_50.xlsx ├── cgc_aggregate_file_size_by_disease.csv ├── cgc_tcga_disease_type_file_numbers.csv └── draft-logs │ ├── Acute_Myeloid_Leukemia_workflow.log │ ├── Bladder_Urothelial_Carcinoma_bam2fasta.log │ ├── Brain_Lower_Grade_Glioma_bam2fasta.log │ ├── Brain_Lower_Grade_Glioma_workflow.log │ ├── Breast_Invasive_Carcinoma_bam2fasta.log │ ├── Breast_Invasive_Carcinoma_workflow.log │ ├── Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma_bam2fasta.log │ ├── Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma_workflow.log │ ├── Colon_Adenocarcinoma_bam2fasta.log │ ├── Colon_Adenocarcinoma_workflow.log │ ├── Esophageal_Carcinoma_bam2fasta.log │ ├── Esophageal_Carcinoma_workflow.log │ ├── Glioblastoma_Multiforme_bam2fasta.log │ ├── Glioblastoma_Multiforme_workflow.log │ ├── Head_and_Neck_Squamous_Cell_Carcinoma_bam2fasta.log │ ├── Head_and_Neck_Squamous_Cell_Carcinomama_workflow.log │ ├── Kidney_Chromophobe_bam2fasta.log │ ├── Kidney_Chromophobe_workflow.log │ ├── Kidney_Renal_Clear_Cell_Carcinoma_bam2fasta.log │ ├── Kidney_Renal_Clear_Cell_Carcinoma_workflow.log │ ├── Kidney_Renal_Papillary_Cell_Carcinoma_bam2fasta.log │ ├── Kidney_Renal_Papillary_Cell_Carcinoma_workflow.log │ ├── Liver_Hepatocellular_Carcinoma_bam2fasta.log │ ├── Liver_Hepatocellular_Carcinoma_workflow.log │ ├── Lung_Adenocarcinoma_bam2fasta.log │ ├── Lung_Adenocarcinoma_workflow.log │ ├── Lung_Squamous_Cell_Carcinoma_bam2fasta.log │ ├── Lung_Squamous_Cell_Carcinoma_workflow.log │ ├── Lymphoid_Neoplasm.log │ ├── Lymphoid_Neoplasm_Diffuse_Large_B-cell_Lymphoma_bam2fasta.log │ ├── Ovarian_Serous_Cystadenocarcinoma_bam2fasta.log │ ├── Ovarian_Serous_Cystadenocarcinoma_workflow.log │ ├── Pheochromocytoma_and_Paraganglioma_bam2fasta.log │ ├── Prostate_Adenocarcinoma_bam2fasta.log │ ├── Rectum_Adenocarcinoma_bam2fasta.log │ ├── Rectum_Adenocarcinoma_workflow.log │ ├── Sarcoma_bam2fasta.log │ ├── Sarcoma_workflow.log │ ├── Skin_Cutaneous_Melanoma_workflow.log │ ├── Stomach_Adenocarcinoma_bam2fasta.log │ ├── Stomach_Adenocarcinoma_workflow.log │ ├── Thyroid_Carcinoma_bam2fasta.log │ ├── Thyroid_Carcinoma_workflow.log │ ├── Uterine_Corpus_Endometrial_Carcinoma_workflow.log │ ├── flagstat_Acute_Myeloid_Leukemia.txt │ ├── flagstat_Adrenocortical_Carcinoma.txt │ ├── flagstat_Bladder_Urothelial_Carcinoma.txt │ ├── flagstat_Brain_Lower_Grade_Glioma.txt │ ├── flagstat_Breast_Invasive_Carcinoma.txt │ ├── flagstat_Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma.txt │ ├── flagstat_Cholangiocarcinoma.txt │ ├── flagstat_Colon_Adenocarcinoma.txt │ ├── flagstat_Esophageal_Carcinoma.txt │ ├── flagstat_Glioblastoma_Multiforme.txt │ ├── flagstat_Head_and_Neck_Squamous_Cell_Carcinoma.txt │ ├── flagstat_Kidney_Chromophobe.txt │ ├── flagstat_Kidney_Renal_Clear_Cell_Carcinoma.txt │ ├── flagstat_Kidney_Renal_Papillary_Cell_Carcinoma.txt │ ├── flagstat_Liver_Hepatocellular_Carcinoma.txt │ ├── flagstat_Lung_Adenocarcinoma.txt │ ├── flagstat_Lung_Squamous_Cell_Carcinoma.txt │ ├── flagstat_Lymphoid_Neoplasm_Diffuse_Large_2DB-cell_Lymphoma.txt │ ├── flagstat_Mesothelioma.txt │ ├── flagstat_Ovarian_Serous_Cystadenocarcinoma.txt │ ├── flagstat_Pancreatic_Adenocarcinoma.txt │ ├── flagstat_Pheochromocytoma_and_Paraganglioma.txt │ ├── flagstat_Prostate_Adenocarcinoma.txt │ ├── flagstat_Rectum_Adenocarcinoma.txt │ ├── flagstat_Sarcoma.txt │ ├── flagstat_Skin_Cutaneous_Melanoma.txt │ ├── flagstat_Stomach_Adenocarcinoma.txt │ ├── flagstat_Testicular_Germ_Cell_Tumors.txt │ ├── flagstat_Thymoma.txt │ ├── flagstat_Thyroid_Carcinoma.txt │ ├── flagstat_Uterine_Carcinosarcoma.txt │ ├── flagstat_Uterine_Corpus_Endometrial_Carcinoma.txt │ └── flagstat_Uveal_Melanoma.txt ├── docker ├── .DS_Store ├── braken_docker │ ├── Dockerfile │ ├── LICENSE │ ├── README │ ├── count-kmer-abundances.pl │ ├── est_abundance.py │ ├── generate_kmer_distribution.py │ └── sample_data │ │ ├── sample_kmer_distr_75mers.txt │ │ ├── sample_output_bracken.report │ │ ├── sample_output_species_abundance.txt │ │ └── sample_test.report ├── centrifuge_docker │ └── Dockerfile ├── docker-parse-kraken-to-biom │ ├── Dockerfile │ ├── parse_kraken_to_biom.py │ ├── requirements.txt │ └── test_parse_kraken_to_biom.py ├── docker-parse-kraken-to-fasta │ ├── Dockerfile │ ├── Dockerfile~ │ ├── __pycache__ │ │ └── kraken_to_fasta.cpython-35.pyc │ ├── kraken_to_fasta.py │ ├── requirements.txt │ ├── requirements.txt~ │ └── test_kraken_to_fasta.py ├── docker-qiime │ ├── Dockerfile │ ├── downstream.sh │ ├── qiime_config │ └── upstream.sh ├── kraken_docker │ ├── .DS_Store │ └── Dockerfile └── meta2qiime_docker │ ├── Dockerfile │ ├── READMEDocker.md │ └── cgc_metadata_to_qiime_mapping_file.py ├── jupyter_notebooks ├── Plasma Kraken Machine Learning LOO Analysis.ipynb ├── Plasma SHOGUN Machine Learning LOO Analysis.ipynb ├── TCGA Batch Correction -- Final Analysis.ipynb ├── TCGA Data IO v3 GDP091318.ipynb ├── TCGA Validation Spits Batch Correction -- Final Analysis.ipynb └── cgc_sparql_3D_dict_arrays.ipynb ├── metadata ├── .DS_Store ├── firehose_tcga_metadata │ ├── .DS_Store │ ├── Full_Joined_CDEs.csv │ ├── Intersected_CDEs.csv │ └── by_disease │ │ ├── joinedMetaDF_Cholangiocarcinoma.csv │ │ └── joinedMetaDF_PancreaticAdenocarcinoma.csv ├── meta2qiime_mapping_file │ ├── README.md │ ├── cgc_qiime_mapping_file_18154_files.txt │ └── cgc_qiime_mapping_file_18154_files_incl_SPARQL_columns.txt └── sparql_query_and_jupyter_notebok_metadata │ ├── caseGroupedDict.p │ ├── fileGroupedDict.p │ └── mergedCGCMetadata_tcga_microbiome.csv ├── python_scripts ├── add_metadata_columns.py ├── cgc_compare_files.py ├── cgc_compute_stats.py ├── cgc_create_tcga_workflow_task.py ├── cgc_create_viral_output_task.py ├── cgc_get_download_links.py ├── cgc_metadata_to_qiime_mapping_file.py ├── cgc_python_api_by_disease_type.py ├── cgc_samtools_bam2fasta_worklfow_task.py ├── cgc_sparql_metadata_python_api.py ├── commands.txt ├── kraken_to_fasta.py ├── make_merged_CDE_table.py ├── parse_kraken_to_biom.py ├── process_fasta_stats.py ├── rename_sample_ids.py ├── repophlan_genomeID_taxonomy.py ├── runChunksTemplate_size.py ├── solve_Stomach_Adenocarcinoma.py ├── split_wgs_rnaseq.py ├── sum_read_counts.py ├── sum_stats_counts.py ├── test_1.txt ├── test_2.txt ├── test_biom.biom ├── test_biom.txt ├── tests │ ├── .DS_Store │ ├── test_cgc_bowtie2_build.py │ ├── test_cgc_create_tcga_workflow_task.py │ ├── test_kraken_to_fasta.py │ └── test_parse_kraken_to_biom.py ├── unittest_cgc_python_api_by_disease_type.py ├── validate_sum_stats.py └── yaml_test_config.yaml ├── r_scripts ├── .DS_Store ├── All_Tumor_ML_predict_LvsH_tumor_stageFA.R ├── All_Tumor_ML_predict_cancer_1VsAllFA_Patent.R ├── All_Tumor_ML_predict_tumor_vs_normal_FA_Patent.R ├── All_Tumor_batch_analysisFA.R ├── All_Tumor_clinical_analysesFA.R ├── Bubble-Plots-of-Spiked-Pseudo-Contaminant-Feature-Importance.R ├── Decontamination-by-Plate-Center-Combination.R ├── Machine-Learning-Performance-Vs-Minority-Class.R ├── Plasma-Bootstrap500-Machine-Learning.R ├── Plasma-Subsampling-Machine-Learning-100Iterations.R ├── Plasma-Voom-SNM-Normalize-Age-and-Sex.R ├── Plasma-age-regression-loocv.R ├── Plasma-permutation-testing-age-and-sex.R ├── Run-All-TCGA-Machine-Learning-Comparisons-Across-All-Decontaminated-Data-Types.R ├── TCGA-Simulation-for-Estimating-Plasma-Experiment-Sample-Size-Example-HMS-Kraken.R ├── Tumor_Microbe_SubtypingFA.R ├── Validation_Data_Splits_and_Model_Testing.R ├── cgc_sparql_metadata_r_api.R ├── predCancer1VsAllFA_Patent.R ├── predTumorVsNormalFA_Patent.R ├── tcga-website-rshiny-app.R ├── validationPredCancer1VsAllFA.R └── validationPredTumorVsNormalFA.R ├── repophlan_database ├── README.md ├── repophlan_microbes_wscores_k__Bacteria_k__Archaea_screen.txt └── repophlan_microbes_wscores_k__Viruses_k__Viroids_all.txt ├── shell_scripts ├── Example-SHOGUN-Run-TCGA-Lung-Cancer.sh ├── Pull_metadata_from_Firehose.sh ├── kraken_translate.sh ├── run_download.sh ├── run_flagstat_stats.sh ├── sum_read_counts.sh ├── tcga_bwa_alignment.sh ├── tcga_filter_Kraken_MPA.sh ├── tcga_full_biom_diversity.sh ├── tcga_make_biom_table.py ├── tcga_make_biom_table.sh ├── tcga_make_biom_table_from_Kraken_output.sh ├── tcga_make_biom_table_per_disease_type.sh └── tcga_merge_biom_tables.sh ├── source_tracker_scripts ├── .DS_Store ├── stNormalCOAD.qsub └── stSKCMPrimaryTumor ├── sparql_queries ├── cgcFileNameCount.rq ├── cgcFileSizeByDisease.rq ├── cgcFileSizeSum.rq ├── cgcMetadataSparqlQuery.rq └── cgcMetadataSparqlQueryShort.rq └── speedtest-cli /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/.DS_Store -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/README.md -------------------------------------------------------------------------------- /cgc/Mapping_file_lucky_50.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/Mapping_file_lucky_50.txt -------------------------------------------------------------------------------- /cgc/Mapping_file_lucky_50.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/Mapping_file_lucky_50.xlsx -------------------------------------------------------------------------------- /cgc/cgc_aggregate_file_size_by_disease.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/cgc_aggregate_file_size_by_disease.csv -------------------------------------------------------------------------------- /cgc/cgc_tcga_disease_type_file_numbers.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/cgc_tcga_disease_type_file_numbers.csv -------------------------------------------------------------------------------- /cgc/draft-logs/Acute_Myeloid_Leukemia_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Acute_Myeloid_Leukemia_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Bladder_Urothelial_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Bladder_Urothelial_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Brain_Lower_Grade_Glioma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Brain_Lower_Grade_Glioma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Brain_Lower_Grade_Glioma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Brain_Lower_Grade_Glioma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Breast_Invasive_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Breast_Invasive_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Breast_Invasive_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Breast_Invasive_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Colon_Adenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Colon_Adenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Colon_Adenocarcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Colon_Adenocarcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Esophageal_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Esophageal_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Esophageal_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Esophageal_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Glioblastoma_Multiforme_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Glioblastoma_Multiforme_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Glioblastoma_Multiforme_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Glioblastoma_Multiforme_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Head_and_Neck_Squamous_Cell_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Head_and_Neck_Squamous_Cell_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Head_and_Neck_Squamous_Cell_Carcinomama_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Head_and_Neck_Squamous_Cell_Carcinomama_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Kidney_Chromophobe_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Kidney_Chromophobe_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Kidney_Chromophobe_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Kidney_Chromophobe_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Kidney_Renal_Clear_Cell_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Kidney_Renal_Clear_Cell_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Kidney_Renal_Clear_Cell_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Kidney_Renal_Clear_Cell_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Kidney_Renal_Papillary_Cell_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Kidney_Renal_Papillary_Cell_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Kidney_Renal_Papillary_Cell_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Kidney_Renal_Papillary_Cell_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Liver_Hepatocellular_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Liver_Hepatocellular_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Liver_Hepatocellular_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Liver_Hepatocellular_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Lung_Adenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Lung_Adenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Lung_Adenocarcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Lung_Adenocarcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Lung_Squamous_Cell_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Lung_Squamous_Cell_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Lung_Squamous_Cell_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Lung_Squamous_Cell_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Lymphoid_Neoplasm.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Lymphoid_Neoplasm.log -------------------------------------------------------------------------------- /cgc/draft-logs/Lymphoid_Neoplasm_Diffuse_Large_B-cell_Lymphoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Lymphoid_Neoplasm_Diffuse_Large_B-cell_Lymphoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Ovarian_Serous_Cystadenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Ovarian_Serous_Cystadenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Ovarian_Serous_Cystadenocarcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Ovarian_Serous_Cystadenocarcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Pheochromocytoma_and_Paraganglioma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Pheochromocytoma_and_Paraganglioma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Prostate_Adenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Prostate_Adenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Rectum_Adenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Rectum_Adenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Rectum_Adenocarcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Rectum_Adenocarcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Sarcoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Sarcoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Sarcoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Sarcoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Skin_Cutaneous_Melanoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Skin_Cutaneous_Melanoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Stomach_Adenocarcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Stomach_Adenocarcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Stomach_Adenocarcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Stomach_Adenocarcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Thyroid_Carcinoma_bam2fasta.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Thyroid_Carcinoma_bam2fasta.log -------------------------------------------------------------------------------- /cgc/draft-logs/Thyroid_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Thyroid_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/Uterine_Corpus_Endometrial_Carcinoma_workflow.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/Uterine_Corpus_Endometrial_Carcinoma_workflow.log -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Acute_Myeloid_Leukemia.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Acute_Myeloid_Leukemia.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Adrenocortical_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Adrenocortical_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Bladder_Urothelial_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Bladder_Urothelial_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Brain_Lower_Grade_Glioma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Brain_Lower_Grade_Glioma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Breast_Invasive_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Breast_Invasive_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Cervical_Squamous_Cell_Carcinoma_and_Endocervical_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Cholangiocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Cholangiocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Colon_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Colon_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Esophageal_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Esophageal_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Glioblastoma_Multiforme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Glioblastoma_Multiforme.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Head_and_Neck_Squamous_Cell_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Head_and_Neck_Squamous_Cell_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Kidney_Chromophobe.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Kidney_Chromophobe.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Kidney_Renal_Clear_Cell_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Kidney_Renal_Clear_Cell_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Kidney_Renal_Papillary_Cell_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Kidney_Renal_Papillary_Cell_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Liver_Hepatocellular_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Liver_Hepatocellular_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Lung_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Lung_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Lung_Squamous_Cell_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Lung_Squamous_Cell_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Lymphoid_Neoplasm_Diffuse_Large_2DB-cell_Lymphoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Lymphoid_Neoplasm_Diffuse_Large_2DB-cell_Lymphoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Mesothelioma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Mesothelioma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Ovarian_Serous_Cystadenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Ovarian_Serous_Cystadenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Pancreatic_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Pancreatic_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Pheochromocytoma_and_Paraganglioma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Pheochromocytoma_and_Paraganglioma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Prostate_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Prostate_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Rectum_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Rectum_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Sarcoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Sarcoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Skin_Cutaneous_Melanoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Skin_Cutaneous_Melanoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Stomach_Adenocarcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Stomach_Adenocarcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Testicular_Germ_Cell_Tumors.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Testicular_Germ_Cell_Tumors.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Thymoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Thymoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Thyroid_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Thyroid_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Uterine_Carcinosarcoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Uterine_Carcinosarcoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Uterine_Corpus_Endometrial_Carcinoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Uterine_Corpus_Endometrial_Carcinoma.txt -------------------------------------------------------------------------------- /cgc/draft-logs/flagstat_Uveal_Melanoma.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/cgc/draft-logs/flagstat_Uveal_Melanoma.txt -------------------------------------------------------------------------------- /docker/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/.DS_Store -------------------------------------------------------------------------------- /docker/braken_docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/Dockerfile -------------------------------------------------------------------------------- /docker/braken_docker/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/LICENSE -------------------------------------------------------------------------------- /docker/braken_docker/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/README -------------------------------------------------------------------------------- /docker/braken_docker/count-kmer-abundances.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/count-kmer-abundances.pl -------------------------------------------------------------------------------- /docker/braken_docker/est_abundance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/est_abundance.py -------------------------------------------------------------------------------- /docker/braken_docker/generate_kmer_distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/generate_kmer_distribution.py -------------------------------------------------------------------------------- /docker/braken_docker/sample_data/sample_kmer_distr_75mers.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/sample_data/sample_kmer_distr_75mers.txt -------------------------------------------------------------------------------- /docker/braken_docker/sample_data/sample_output_bracken.report: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/sample_data/sample_output_bracken.report -------------------------------------------------------------------------------- /docker/braken_docker/sample_data/sample_output_species_abundance.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/sample_data/sample_output_species_abundance.txt -------------------------------------------------------------------------------- /docker/braken_docker/sample_data/sample_test.report: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/braken_docker/sample_data/sample_test.report -------------------------------------------------------------------------------- /docker/centrifuge_docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/centrifuge_docker/Dockerfile -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-biom/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-biom/Dockerfile -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-biom/parse_kraken_to_biom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-biom/parse_kraken_to_biom.py -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-biom/requirements.txt: -------------------------------------------------------------------------------- 1 | pandas 2 | click 3 | biom-format -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-biom/test_parse_kraken_to_biom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-biom/test_parse_kraken_to_biom.py -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-fasta/Dockerfile -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/Dockerfile~: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-fasta/Dockerfile~ -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/__pycache__/kraken_to_fasta.cpython-35.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-fasta/__pycache__/kraken_to_fasta.cpython-35.pyc -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/kraken_to_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-fasta/kraken_to_fasta.py -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/requirements.txt: -------------------------------------------------------------------------------- 1 | scikit-bio 2 | click 3 | -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/requirements.txt~: -------------------------------------------------------------------------------- 1 | click 2 | scikit-bio 3 | -------------------------------------------------------------------------------- /docker/docker-parse-kraken-to-fasta/test_kraken_to_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-parse-kraken-to-fasta/test_kraken_to_fasta.py -------------------------------------------------------------------------------- /docker/docker-qiime/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-qiime/Dockerfile -------------------------------------------------------------------------------- /docker/docker-qiime/downstream.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-qiime/downstream.sh -------------------------------------------------------------------------------- /docker/docker-qiime/qiime_config: -------------------------------------------------------------------------------- 1 | temp_dir /data/scratch/ 2 | -------------------------------------------------------------------------------- /docker/docker-qiime/upstream.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/docker-qiime/upstream.sh -------------------------------------------------------------------------------- /docker/kraken_docker/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/kraken_docker/.DS_Store -------------------------------------------------------------------------------- /docker/kraken_docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/kraken_docker/Dockerfile -------------------------------------------------------------------------------- /docker/meta2qiime_docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/meta2qiime_docker/Dockerfile -------------------------------------------------------------------------------- /docker/meta2qiime_docker/READMEDocker.md: -------------------------------------------------------------------------------- 1 | # tcga/docker 2 | Microbial analysis in TCGA data 3 | -------------------------------------------------------------------------------- /docker/meta2qiime_docker/cgc_metadata_to_qiime_mapping_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/docker/meta2qiime_docker/cgc_metadata_to_qiime_mapping_file.py -------------------------------------------------------------------------------- /jupyter_notebooks/Plasma Kraken Machine Learning LOO Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/jupyter_notebooks/Plasma Kraken Machine Learning LOO Analysis.ipynb -------------------------------------------------------------------------------- /jupyter_notebooks/Plasma SHOGUN Machine Learning LOO Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/jupyter_notebooks/Plasma SHOGUN Machine Learning LOO Analysis.ipynb -------------------------------------------------------------------------------- /jupyter_notebooks/TCGA Batch Correction -- Final Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/jupyter_notebooks/TCGA Batch Correction -- Final Analysis.ipynb -------------------------------------------------------------------------------- /jupyter_notebooks/TCGA Data IO v3 GDP091318.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/jupyter_notebooks/TCGA Data IO v3 GDP091318.ipynb -------------------------------------------------------------------------------- /jupyter_notebooks/TCGA Validation Spits Batch Correction -- Final Analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/jupyter_notebooks/TCGA Validation Spits Batch Correction -- Final Analysis.ipynb -------------------------------------------------------------------------------- /jupyter_notebooks/cgc_sparql_3D_dict_arrays.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/jupyter_notebooks/cgc_sparql_3D_dict_arrays.ipynb -------------------------------------------------------------------------------- /metadata/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/.DS_Store -------------------------------------------------------------------------------- /metadata/firehose_tcga_metadata/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/firehose_tcga_metadata/.DS_Store -------------------------------------------------------------------------------- /metadata/firehose_tcga_metadata/Full_Joined_CDEs.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/firehose_tcga_metadata/Full_Joined_CDEs.csv -------------------------------------------------------------------------------- /metadata/firehose_tcga_metadata/Intersected_CDEs.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/firehose_tcga_metadata/Intersected_CDEs.csv -------------------------------------------------------------------------------- /metadata/firehose_tcga_metadata/by_disease/joinedMetaDF_Cholangiocarcinoma.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/firehose_tcga_metadata/by_disease/joinedMetaDF_Cholangiocarcinoma.csv -------------------------------------------------------------------------------- /metadata/firehose_tcga_metadata/by_disease/joinedMetaDF_PancreaticAdenocarcinoma.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/firehose_tcga_metadata/by_disease/joinedMetaDF_PancreaticAdenocarcinoma.csv -------------------------------------------------------------------------------- /metadata/meta2qiime_mapping_file/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/meta2qiime_mapping_file/README.md -------------------------------------------------------------------------------- /metadata/meta2qiime_mapping_file/cgc_qiime_mapping_file_18154_files.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/meta2qiime_mapping_file/cgc_qiime_mapping_file_18154_files.txt -------------------------------------------------------------------------------- /metadata/meta2qiime_mapping_file/cgc_qiime_mapping_file_18154_files_incl_SPARQL_columns.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/meta2qiime_mapping_file/cgc_qiime_mapping_file_18154_files_incl_SPARQL_columns.txt -------------------------------------------------------------------------------- /metadata/sparql_query_and_jupyter_notebok_metadata/caseGroupedDict.p: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/sparql_query_and_jupyter_notebok_metadata/caseGroupedDict.p -------------------------------------------------------------------------------- /metadata/sparql_query_and_jupyter_notebok_metadata/fileGroupedDict.p: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/sparql_query_and_jupyter_notebok_metadata/fileGroupedDict.p -------------------------------------------------------------------------------- /metadata/sparql_query_and_jupyter_notebok_metadata/mergedCGCMetadata_tcga_microbiome.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/metadata/sparql_query_and_jupyter_notebok_metadata/mergedCGCMetadata_tcga_microbiome.csv -------------------------------------------------------------------------------- /python_scripts/add_metadata_columns.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/add_metadata_columns.py -------------------------------------------------------------------------------- /python_scripts/cgc_compare_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_compare_files.py -------------------------------------------------------------------------------- /python_scripts/cgc_compute_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_compute_stats.py -------------------------------------------------------------------------------- /python_scripts/cgc_create_tcga_workflow_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_create_tcga_workflow_task.py -------------------------------------------------------------------------------- /python_scripts/cgc_create_viral_output_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_create_viral_output_task.py -------------------------------------------------------------------------------- /python_scripts/cgc_get_download_links.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_get_download_links.py -------------------------------------------------------------------------------- /python_scripts/cgc_metadata_to_qiime_mapping_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_metadata_to_qiime_mapping_file.py -------------------------------------------------------------------------------- /python_scripts/cgc_python_api_by_disease_type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_python_api_by_disease_type.py -------------------------------------------------------------------------------- /python_scripts/cgc_samtools_bam2fasta_worklfow_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_samtools_bam2fasta_worklfow_task.py -------------------------------------------------------------------------------- /python_scripts/cgc_sparql_metadata_python_api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/cgc_sparql_metadata_python_api.py -------------------------------------------------------------------------------- /python_scripts/commands.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/commands.txt -------------------------------------------------------------------------------- /python_scripts/kraken_to_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/kraken_to_fasta.py -------------------------------------------------------------------------------- /python_scripts/make_merged_CDE_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/make_merged_CDE_table.py -------------------------------------------------------------------------------- /python_scripts/parse_kraken_to_biom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/parse_kraken_to_biom.py -------------------------------------------------------------------------------- /python_scripts/process_fasta_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/process_fasta_stats.py -------------------------------------------------------------------------------- /python_scripts/rename_sample_ids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/rename_sample_ids.py -------------------------------------------------------------------------------- /python_scripts/repophlan_genomeID_taxonomy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/repophlan_genomeID_taxonomy.py -------------------------------------------------------------------------------- /python_scripts/runChunksTemplate_size.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/runChunksTemplate_size.py -------------------------------------------------------------------------------- /python_scripts/solve_Stomach_Adenocarcinoma.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/solve_Stomach_Adenocarcinoma.py -------------------------------------------------------------------------------- /python_scripts/split_wgs_rnaseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/split_wgs_rnaseq.py -------------------------------------------------------------------------------- /python_scripts/sum_read_counts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/sum_read_counts.py -------------------------------------------------------------------------------- /python_scripts/sum_stats_counts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/sum_stats_counts.py -------------------------------------------------------------------------------- /python_scripts/test_1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/test_1.txt -------------------------------------------------------------------------------- /python_scripts/test_2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/test_2.txt -------------------------------------------------------------------------------- /python_scripts/test_biom.biom: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/test_biom.biom -------------------------------------------------------------------------------- /python_scripts/test_biom.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/test_biom.txt -------------------------------------------------------------------------------- /python_scripts/tests/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/tests/.DS_Store -------------------------------------------------------------------------------- /python_scripts/tests/test_cgc_bowtie2_build.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/tests/test_cgc_bowtie2_build.py -------------------------------------------------------------------------------- /python_scripts/tests/test_cgc_create_tcga_workflow_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/tests/test_cgc_create_tcga_workflow_task.py -------------------------------------------------------------------------------- /python_scripts/tests/test_kraken_to_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/tests/test_kraken_to_fasta.py -------------------------------------------------------------------------------- /python_scripts/tests/test_parse_kraken_to_biom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/tests/test_parse_kraken_to_biom.py -------------------------------------------------------------------------------- /python_scripts/unittest_cgc_python_api_by_disease_type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/unittest_cgc_python_api_by_disease_type.py -------------------------------------------------------------------------------- /python_scripts/validate_sum_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/validate_sum_stats.py -------------------------------------------------------------------------------- /python_scripts/yaml_test_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/python_scripts/yaml_test_config.yaml -------------------------------------------------------------------------------- /r_scripts/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/.DS_Store -------------------------------------------------------------------------------- /r_scripts/All_Tumor_ML_predict_LvsH_tumor_stageFA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/All_Tumor_ML_predict_LvsH_tumor_stageFA.R -------------------------------------------------------------------------------- /r_scripts/All_Tumor_ML_predict_cancer_1VsAllFA_Patent.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/All_Tumor_ML_predict_cancer_1VsAllFA_Patent.R -------------------------------------------------------------------------------- /r_scripts/All_Tumor_ML_predict_tumor_vs_normal_FA_Patent.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/All_Tumor_ML_predict_tumor_vs_normal_FA_Patent.R -------------------------------------------------------------------------------- /r_scripts/All_Tumor_batch_analysisFA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/All_Tumor_batch_analysisFA.R -------------------------------------------------------------------------------- /r_scripts/All_Tumor_clinical_analysesFA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/All_Tumor_clinical_analysesFA.R -------------------------------------------------------------------------------- /r_scripts/Bubble-Plots-of-Spiked-Pseudo-Contaminant-Feature-Importance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Bubble-Plots-of-Spiked-Pseudo-Contaminant-Feature-Importance.R -------------------------------------------------------------------------------- /r_scripts/Decontamination-by-Plate-Center-Combination.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Decontamination-by-Plate-Center-Combination.R -------------------------------------------------------------------------------- /r_scripts/Machine-Learning-Performance-Vs-Minority-Class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Machine-Learning-Performance-Vs-Minority-Class.R -------------------------------------------------------------------------------- /r_scripts/Plasma-Bootstrap500-Machine-Learning.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Plasma-Bootstrap500-Machine-Learning.R -------------------------------------------------------------------------------- /r_scripts/Plasma-Subsampling-Machine-Learning-100Iterations.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Plasma-Subsampling-Machine-Learning-100Iterations.R -------------------------------------------------------------------------------- /r_scripts/Plasma-Voom-SNM-Normalize-Age-and-Sex.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Plasma-Voom-SNM-Normalize-Age-and-Sex.R -------------------------------------------------------------------------------- /r_scripts/Plasma-age-regression-loocv.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Plasma-age-regression-loocv.R -------------------------------------------------------------------------------- /r_scripts/Plasma-permutation-testing-age-and-sex.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Plasma-permutation-testing-age-and-sex.R -------------------------------------------------------------------------------- /r_scripts/Run-All-TCGA-Machine-Learning-Comparisons-Across-All-Decontaminated-Data-Types.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Run-All-TCGA-Machine-Learning-Comparisons-Across-All-Decontaminated-Data-Types.R -------------------------------------------------------------------------------- /r_scripts/TCGA-Simulation-for-Estimating-Plasma-Experiment-Sample-Size-Example-HMS-Kraken.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/TCGA-Simulation-for-Estimating-Plasma-Experiment-Sample-Size-Example-HMS-Kraken.R -------------------------------------------------------------------------------- /r_scripts/Tumor_Microbe_SubtypingFA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Tumor_Microbe_SubtypingFA.R -------------------------------------------------------------------------------- /r_scripts/Validation_Data_Splits_and_Model_Testing.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/Validation_Data_Splits_and_Model_Testing.R -------------------------------------------------------------------------------- /r_scripts/cgc_sparql_metadata_r_api.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/cgc_sparql_metadata_r_api.R -------------------------------------------------------------------------------- /r_scripts/predCancer1VsAllFA_Patent.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/predCancer1VsAllFA_Patent.R -------------------------------------------------------------------------------- /r_scripts/predTumorVsNormalFA_Patent.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/predTumorVsNormalFA_Patent.R -------------------------------------------------------------------------------- /r_scripts/tcga-website-rshiny-app.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/tcga-website-rshiny-app.R -------------------------------------------------------------------------------- /r_scripts/validationPredCancer1VsAllFA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/validationPredCancer1VsAllFA.R -------------------------------------------------------------------------------- /r_scripts/validationPredTumorVsNormalFA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/r_scripts/validationPredTumorVsNormalFA.R -------------------------------------------------------------------------------- /repophlan_database/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/repophlan_database/README.md -------------------------------------------------------------------------------- /repophlan_database/repophlan_microbes_wscores_k__Bacteria_k__Archaea_screen.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/repophlan_database/repophlan_microbes_wscores_k__Bacteria_k__Archaea_screen.txt -------------------------------------------------------------------------------- /repophlan_database/repophlan_microbes_wscores_k__Viruses_k__Viroids_all.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/repophlan_database/repophlan_microbes_wscores_k__Viruses_k__Viroids_all.txt -------------------------------------------------------------------------------- /shell_scripts/Example-SHOGUN-Run-TCGA-Lung-Cancer.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/Example-SHOGUN-Run-TCGA-Lung-Cancer.sh -------------------------------------------------------------------------------- /shell_scripts/Pull_metadata_from_Firehose.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/Pull_metadata_from_Firehose.sh -------------------------------------------------------------------------------- /shell_scripts/kraken_translate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/kraken_translate.sh -------------------------------------------------------------------------------- /shell_scripts/run_download.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/run_download.sh -------------------------------------------------------------------------------- /shell_scripts/run_flagstat_stats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/run_flagstat_stats.sh -------------------------------------------------------------------------------- /shell_scripts/sum_read_counts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/sum_read_counts.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_bwa_alignment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_bwa_alignment.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_filter_Kraken_MPA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_filter_Kraken_MPA.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_full_biom_diversity.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_full_biom_diversity.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_make_biom_table.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /shell_scripts/tcga_make_biom_table.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_make_biom_table.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_make_biom_table_from_Kraken_output.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_make_biom_table_from_Kraken_output.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_make_biom_table_per_disease_type.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_make_biom_table_per_disease_type.sh -------------------------------------------------------------------------------- /shell_scripts/tcga_merge_biom_tables.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/shell_scripts/tcga_merge_biom_tables.sh -------------------------------------------------------------------------------- /source_tracker_scripts/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/source_tracker_scripts/.DS_Store -------------------------------------------------------------------------------- /source_tracker_scripts/stNormalCOAD.qsub: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/source_tracker_scripts/stNormalCOAD.qsub -------------------------------------------------------------------------------- /source_tracker_scripts/stSKCMPrimaryTumor: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/source_tracker_scripts/stSKCMPrimaryTumor -------------------------------------------------------------------------------- /sparql_queries/cgcFileNameCount.rq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/sparql_queries/cgcFileNameCount.rq -------------------------------------------------------------------------------- /sparql_queries/cgcFileSizeByDisease.rq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/sparql_queries/cgcFileSizeByDisease.rq -------------------------------------------------------------------------------- /sparql_queries/cgcFileSizeSum.rq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/sparql_queries/cgcFileSizeSum.rq -------------------------------------------------------------------------------- /sparql_queries/cgcMetadataSparqlQuery.rq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/sparql_queries/cgcMetadataSparqlQuery.rq -------------------------------------------------------------------------------- /sparql_queries/cgcMetadataSparqlQueryShort.rq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/sparql_queries/cgcMetadataSparqlQueryShort.rq -------------------------------------------------------------------------------- /speedtest-cli: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biocore/tcga/HEAD/speedtest-cli --------------------------------------------------------------------------------