marcsaric > rna-seq cancer-research

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1Download | CGGA - Chinese Glioma Genome Atlas
http://www.cgga.org.cn/download.jsp
4 years ago by @marcsaric
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CGGA
cancer-research
database
exome
glioblastoma
glioma
methylation
rna-seq
transcriptome
CGGAcancer-researchdatabaseexomeglioblastomagliomamethylationrna-seqtranscriptome
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1RPubs - DESeq2 experimental design and interpretation
https://rpubs.com/ge600/deseq2
5 years ago by @marcsaric
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deseq2
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1r - Understanding DESeq2 design, contrast and results - Bioinformatics Stack Exchange
https://bioinformatics.stackexchange.com/questions/153/understanding-deseq2-design-contrast-and-results
5 years ago by @marcsaric
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1dranew / defuse — Bitbucket
https://bitbucket.org/dranew/defuse/src/master/
5 years ago by @marcsaric
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LGG
cancer-research
fusion-genes
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tcga-lgg
LGGcancer-researchfusion-genesrna-seqshouldreadsoftwaretcga-lgg
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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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cancer-researchfulltextgdcpan-cancerpaperrna-seqshouldreadtcga
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publications (hide)36
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1MuSiC: Identifying mutational significance in cancer genomes
N. Dees, Q. Zhang, C. Kandoth, M. Wendl, W. Schierding, D. Koboldt, T. Mooney, M. Callaway, D. Dooling, E. Mardis and 2 other author(s). Genome Research, 22 (8, /content/22/8.cover.gif): 1589-1598 (2012)
4 years ago by @marcsaric
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cancer-research
drivers
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methylation
pipeline
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wgs
wxs
cancer-researchdriversfulltextmethylationpipelinerna-seqshouldreadsoftwarewgswxs
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1Transcriptome analysis reveals distinct gene expression profiles in astrocytoma grades II-IV
N. Narsia, P. Ramagiri, J. Ehrmann, and Z. Kolar. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub, 161 (3): 261-271 (September 2017)
4 years ago by @marcsaric
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astrocytoma
cancer-research
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geo
glioma
rna-seq
shouldread
astrocytomacancer-researchfulltextgeogliomarna-seqshouldread
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5Mining Cancer Transcriptomes: Bioinformatic Tools and the Remaining Challenges
T. Milan, and B. Wilhelm. Mol Diagn Ther, 21 (3): 249-258 (June 2017)
4 years ago by @marcsaric
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cancer-research
review
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cancer-researchreviewrna-seqshouldreadsoftware
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1Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas
Z. Zhao, F. Meng, W. Wang, Z. Wang, C. Zhang, and T. Jiang. Scientific Data, 4 (1): 170024-- (2017)
4 years ago by @marcsaric
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cancer-research
fulltext
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cancer-researchfulltextrna-seqshouldread
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1Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma
J. Zhu, and Y. Zhang. PeerJ, (2019)
4 years ago by @marcsaric
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cancer-research
fulltext
glioma
mustread
rna-seq
survival
cancer-researchfulltextgliomamustreadrna-seqsurvival
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1Thirty biologically interpretable clusters of transcription factors distinguish cancer type
Z. Abrams, M. Zucker, M. Wang, A. Asiaee Taheri, L. Abruzzo, and K. Coombes. BMC Genomics, 19 (1): 738-738 (October 2018)
4 years ago by @marcsaric
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1Using Supervised Learning Methods for Gene Selection in RNA-Seq Case-Control Studies
S. Wenric, and R. Shemirani. Frontiers in Genetics, (August 2018)
5 years ago by @marcsaric
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cancer-research
fulltext
machine-learning
rna-seq
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survival
cancer-researchfulltextmachine-learningrna-seqshouldreadsoftwaresurvival
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1Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue
D. Sinicropi, K. Qu, F. Collin, M. Crager, M. Liu, R. Pelham, M. Pho, A. Rossi, J. Jeong, A. Scott and 7 other author(s). PLOS ONE, 7 (7): 1-10 (July 2012)
5 years ago by @marcsaric
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cancer-research
ffpe
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cancer-researchffpefulltextrna-seqshouldreadsoftware
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2Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
S. Graw, R. Meier, K. Minn, C. Bloomer, A. Godwin, B. Fridley, A. Vlad, P. Beyerlein, and J. Chien. Scientific Reports, (July 2015)
5 years ago by @marcsaric
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deseq2
ff
ffpe
fulltext
rna-seq
benchmarkcancer-researchdeseq2ffffpefulltextrna-seq
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1Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples
J. Zhu, N. Deane, K. Lewis, C. Padmanabhan, M. Washington, K. Ciombor, C. Timmers, R. Goldberg, R. Beauchamp, and X. Chen. Scientific Reports, (September 2016)
5 years ago by @marcsaric
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ff
ffpe
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1Sensitivity to BUB1B Inhibition Defines an Alternative Classification of Glioblastoma
E. Lee, M. Pain, H. Wang, J. Herman, C. Toledo, J. DeLuca, R. Yong, P. Paddison, and J. Zhu. Cancer Res, 77 (20): 5518-5529 (October 2017)
5 years ago by @marcsaric
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cancer-research
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glioblastoma
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cancer-researchfastqfulltextglioblastomarna-seqshouldread
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1The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies
P. Zhang, B. Lehmann, Y. Shyr, and Y. Guo. Int J Genomics, (2017)
5 years ago by @marcsaric
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cancer-research
comparison
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2deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
A. McPherson, F. Hormozdiari, A. Zayed, R. Giuliany, G. Ha, M. Sun, M. Griffith, A. Heravi Moussavi, J. Senz, N. Melnyk and 7 other author(s). PLOS Computational Biology, 7 (5): 1-16 (May 2011)
5 years ago by @marcsaric
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cancer-research
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glioma
low-grade
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rna
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tcga
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cancer-researchfulltextgliomalow-grademustreadrnarna-seqsoftwaretcgatcga-lgg
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1Omics Pipe: a community-based framework for reproducible multi-omics data analysis
K. Fisch, T. Mei�ner, L. Gioia, J. Ducom, T. Carland, S. Loguercio, and A. Su. Bioinformatics, 31 (11): 1724-1728 (June 2015)
5 years ago by @marcsaric
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cancer-research
exome
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pipeline
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tcga
wgs
cancer-researchexomefulltextpipelinerna-seqsoftwaretcgawgs
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1Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples
X. Ho, P. Phung, V. Q Le, V. H Nguyen, E. Reimann, E. Prans, G. Kõks, K. Maasalu, N. Le, L. H Trinh and 3 other author(s). Exp Biol Med (Maywood), 242 (18): 1802-1811 (December 2017)
5 years ago by @marcsaric
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cancer-research
fulltext
network-analysis
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transcriptome
cancer-researchfulltextnetwork-analysisrna-seqshouldreadtranscriptome
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1Transcriptomic Analysis of Calcium Remodeling in Colorectal Cancer
E. Pérez-Riesgo, L. Gutiérrez, D. Ubierna, A. Acedo, M. Moyer, L. Núñez, and C. Villalobos. Int J Mol Sci, (April 2017)
5 years ago by @marcsaric
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cancer-research
clustering
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1bcbioRNASeq: R package for bcbio RNA-seq analysis
M. Steinbaugh, L. Pantano, R. Kirchner, V. Barrera, B. Chapman, M. Piper, M. Mistry, R. Khetani, K. Rutherford, O. Hofmann and 2 other author(s). F1000Research, (June 2018)
5 years ago by @marcsaric
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SHOULDREAD
cancer-research
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open-source
pipeline
r-language
rna-seq
software
SHOULDREADcancer-researchfulltextopen-sourcepipeliner-languagerna-seqsoftware
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1Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
I. Tirosh, A. Venteicher, C. Hebert, L. Escalante, A. Patel, K. Yizhak, J. Fisher, C. Rodman, C. Mount, M. Filbin and 28 other author(s). Nature, 539 (7628): 309-313 (November 2016)
5 years ago by @marcsaric
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cancer-research
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rna-seq
shouldread
single-cell-sequencing
cancer-researchfulltextrna-seqshouldreadsingle-cell-sequencing
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1Transforming fusions of FGFR and TACC genes in human glioblastoma
D. Singh, J. Chan, P. Zoppoli, F. Niola, R. Sullivan, A. Castano, E. Liu, J. Reichel, P. Porrati, S. Pellegatta and 14 other author(s). Science, 337 (6099): 1231-1235 (September 2012)
5 years ago by @marcsaric
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cancer-research
fulltext
gene-fusion
rna-seq
shouldread
cancer-researchfulltextgene-fusionrna-seqshouldread
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1RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas
Z. Bao, H. Chen, M. Yang, C. Zhang, K. Yu, W. Ye, B. Hu, W. Yan, W. Zhang, J. Akers and 17 other author(s). Genome Res, 24 (11): 1765-1773 (November 2014)
5 years ago by @marcsaric
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MUSTREAD
cancer-research
fastq
fulltext
gene-fusion
rna-seq
MUSTREADcancer-researchfastqfulltextgene-fusionrna-seq
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1Download | CGGA - Chinese Glioma Genome Atlas

1RPubs - DESeq2 experimental design and interpretation

1r - Understanding DESeq2 design, contrast and results - Bioinformatics Stack Exchange

1dranew / defuse — Bitbucket

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

publications (hide)36
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1MuSiC: Identifying mutational significance in cancer genomes

1Transcriptome analysis reveals distinct gene expression profiles in astrocytoma grades II-IV

5Mining Cancer Transcriptomes: Bioinformatic Tools and the Remaining Challenges

1Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas

1Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma

1Thirty biologically interpretable clusters of transcription factors distinguish cancer type

1Using Supervised Learning Methods for Gene Selection in RNA-Seq Case-Control Studies

1Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

2Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

1Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples

1Sensitivity to BUB1B Inhibition Defines an Alternative Classification of Glioblastoma

1The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies

2deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

1Omics Pipe: a community-based framework for reproducible multi-omics data analysis

1Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples

1Transcriptomic Analysis of Calcium Remodeling in Colorectal Cancer

1bcbioRNASeq: R package for bcbio RNA-seq analysis

1Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

1Transforming fusions of FGFR and TACC genes in human glioblastoma

1RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas

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