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1Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data - PubMed
We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA …
4 years ago by @marcsaric
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1Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. - Abstract - Europe PMC
https://europepmc.org/article/pmc/pmc5467262
4 years ago by @marcsaric
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1GitHub - NCI-GDC/gdc-dnaseq-cwl: CWL for GDC DNASeq workflows
CWL for GDC DNASeq workflows. Contribute to NCI-GDC/gdc-dnaseq-cwl development by creating an account on GitHub.
4 years ago by @marcsaric
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1Oncogenic Signaling Pathways in The Cancer Genome Atlas. - PubMed - NCBI
Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035. Research Support, N.I.H., Extramural
5 years ago by @marcsaric
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1A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. - PubMed - NCBI
Cell. 2018 Apr 5;173(2):386-399.e12. doi: 10.1016/j.cell.2018.03.027. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
5 years ago by @marcsaric
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1Pathogenic Germline Variants in 10,389 Adult Cancers. - PubMed - NCBI
Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. Research Support, Non-U.S. Gov't
5 years ago by @marcsaric
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1Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. - PubMed - NCBI
Cell Rep. 2018 Apr 3;23(1):239-254.e6. doi: 10.1016/j.celrep.2018.03.076.
5 years ago by @marcsaric
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1Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902191/
5 years ago by @marcsaric
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1Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. - PubMed - NCBI
Cell Rep. 2018 Apr 3;23(1):255-269.e4. doi: 10.1016/j.celrep.2018.03.077.
5 years ago by @marcsaric
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1TCGA-Assembler
http://www.compgenome.org/TCGA-Assembler/
6 years ago by @marcsaric
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1google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=2ahUKEwi3rfuUy93eAhVClSwKHdG4BAQQFjABegQIBBAB&url=https%3A%2F%2Fbioconductor.org%2Fhelp%2Fcourse-materials%2F2017%2FBioC2017%2FDay2%2FBOF%2FBioC2017_TCGA_GTEx_BOF%2FREADME.html&usg=AOvVaw1Ilmhk_Ba-h1X7h6epguXW
https://bioconductor.org/help/course-materials/2017/BioC2017/Day2/BOF/BioC2017_TCGA_GTEx_BOF/README.html
6 years ago by @marcsaric
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1The Immune Landscape of Cancer. - PubMed - NCBI
Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.
6 years ago by @marcsaric
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1Comprehensive Characterization of Cancer Driver Genes and Mutations. - PubMed - NCBI
Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060.
6 years ago by @marcsaric
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1Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. - PubMed - NCBI
Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046.
6 years ago by @marcsaric
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1Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. - PubMed - NCBI
Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022.
6 years ago by @marcsaric
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1Common Workflow Language
https://github.com/common-workflow-language
6 years ago by @marcsaric
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1GDC Reference Files | NCI Genomic Data Commons
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files
6 years ago by @marcsaric
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1Bioinformatics Pipeline: Copy Number Variation Analysis - GDC Docs
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/CNV_Pipeline/
6 years ago by @marcsaric
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1Bioinformatics Pipeline: Methylation Liftover Pipeline - GDC Docs
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Methylation_LO_Pipeline/
6 years ago by @marcsaric
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1Bioinformatics Pipeline: mRNA Analysis - GDC Docs
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/
6 years ago by @marcsaric
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1Uniform Genomic Data Analysis in the NCI Genomic Data Commons
Z. Zhang, K. Hernandez, J. Savage, S. Li, D. Miller, S. Agrawal, F. Ortuno, L. Staudt, A. Heath, and R. Grossman. bioRxiv, (2019)
4 years ago by @marcsaric
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1Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
K. Ellrott, M. Bailey, G. Saksena, K. Covington, C. Kandoth, C. Stewart, J. Hess, S. Ma, K. Chiotti, M. McLellan and 730 other author(s). Cell Systems, 6 (3): 271--281.e7 (March 2018)
4 years ago by @marcsaric
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2VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
D. Koboldt, Q. Zhang, D. Larson, D. Shen, M. McLellan, L. Lin, C. Miller, E. Mardis, L. Ding, and R. Wilson. Genome Res, 22 (3): 568-576 (March 2012)
4 years ago by @marcsaric
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3VarScan: variant detection in massively parallel sequencing of individual and pooled samples
D. Koboldt, K. Chen, T. Wylie, D. Larson, M. McLellan, E. Mardis, G. Weinstock, R. Wilson, and L. Ding. Bioinformatics, 25 (17): 2283-2285 (September 2009)
4 years ago by @marcsaric
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2Toward a Shared Vision for Cancer Genomic Data
R. Grossman, A. Heath, V. Ferretti, H. Varmus, D. Lowy, W. Kibbe, and L. Staudt. N Engl J Med, 375 (12): 1109-1112 (September 2016)
4 years ago by @marcsaric
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BibSonomy

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1Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data - PubMed

1Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. - Abstract - Europe PMC

1GitHub - NCI-GDC/gdc-dnaseq-cwl: CWL for GDC DNASeq workflows

1Oncogenic Signaling Pathways in The Cancer Genome Atlas. - PubMed - NCBI

1A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. - PubMed - NCBI

1Pathogenic Germline Variants in 10,389 Adult Cancers. - PubMed - NCBI

1Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. - PubMed - NCBI

1Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

1Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. - PubMed - NCBI

1TCGA-Assembler

1google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=2ahUKEwi3rfuUy93eAhVClSwKHdG4BAQQFjABegQIBBAB&url=https%3A%2F%2Fbioconductor.org%2Fhelp%2Fcourse-materials%2F2017%2FBioC2017%2FDay2%2FBOF%2FBioC2017_TCGA_GTEx_BOF%2FREADME.html&usg=AOvVaw1Ilmhk_Ba-h1X7h6epguXW

1The Immune Landscape of Cancer. - PubMed - NCBI

1Comprehensive Characterization of Cancer Driver Genes and Mutations. - PubMed - NCBI

1Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. - PubMed - NCBI

1Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. - PubMed - NCBI

1Common Workflow Language

1GDC Reference Files | NCI Genomic Data Commons

1Bioinformatics Pipeline: Copy Number Variation Analysis - GDC Docs

1Bioinformatics Pipeline: Methylation Liftover Pipeline - GDC Docs

1Bioinformatics Pipeline: mRNA Analysis - GDC Docs

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1Uniform Genomic Data Analysis in the NCI Genomic Data Commons

1Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

2VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

3VarScan: variant detection in massively parallel sequencing of individual and pooled samples

2Toward a Shared Vision for Cancer Genomic Data

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