-
1
-
-
0035478854
-
Random forests
-
Breiman,L. (2001) Random forests. Mach. Learn., 45, 5-32.
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
2
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard,J.H. et al. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
-
3
-
-
84866002291
-
The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data
-
Cerami,E. et al. (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov., 2, 401-404.
-
(2012)
Cancer Discov.
, vol.2
, pp. 401-404
-
-
Cerami, E.1
-
4
-
-
84885137302
-
Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser
-
Cline,M.S. et al. (2013) Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser. Sci. Rep., 3, 2652.
-
(2013)
Sci. Rep.
, vol.3
, pp. 2652
-
-
Cline, M.S.1
-
5
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
Dillies,M.A. et al. (2013) A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief. Bioinform., 14, 671-683.
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 671-683
-
-
Dillies, M.A.1
-
6
-
-
84907500627
-
RNA-Seq gene profiling - A systematic empirical comparison
-
Fonseca,NA. et al. (2014) RNA-Seq gene profiling - A systematic empirical comparison. PLoS ONE., 9, e107026. doi:10.1371/journal.pone.0107026.
-
(2014)
PLoS ONE
, vol.9
-
-
Fonseca, N.A.1
-
7
-
-
84875740314
-
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal
-
Gao,J. et al. (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal., 6, pl1.
-
(2013)
Sci. Signal.
, vol.6
, pp. l1
-
-
Gao, J.1
-
8
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman,R.C. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
-
(2004)
Genome Biol.
, vol.5
, pp. R80
-
-
Gentleman, R.C.1
-
9
-
-
0001044839
-
Distribution theory for Glass' estimator of effect size and related estimators
-
Hedges,L.V. (1981) Distribution theory for Glass' estimator of effect size and related estimators. J. Edu. Stat., 6, 107-128.
-
(1981)
J. Edu. Stat.
, vol.6
, pp. 107-128
-
-
Hedges, L.V.1
-
11
-
-
56249113343
-
Building predictive models in R using the caret package
-
Kuhn,R.M. (2008) Building predictive models in R using the caret package. J. Stat. Soft., 28, 1-26.
-
(2008)
J. Stat. Soft.
, vol.28
, pp. 1-26
-
-
Kuhn, R.M.1
-
12
-
-
79961123152
-
RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
-
Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
13
-
-
84878580738
-
The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote
-
Liao,Y. et al. (2013) The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res., 41, e108.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e108
-
-
Liao, Y.1
-
14
-
-
84897397058
-
FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
-
Liao,Y. et al. (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923-930.
-
(2014)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
-
15
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
-
Love,M.I. et al. (2014) Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol., 15, 550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
-
16
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi,A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
-
17
-
-
84921425131
-
edgeR for differential RNA-seq and ChIP-seq analysis: An application to stem cell biology
-
Nikolayeva,O. and Robinson,M.D. (2014) edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol. Biol., 1150, 45-79.
-
(2014)
Methods Mol. Biol.
, vol.1150
, pp. 45-79
-
-
Nikolayeva, O.1
Robinson, M.D.2
-
18
-
-
84869890209
-
A single-sample microarray normalization method to facilitate personalized-medicine workflows
-
Piccolo,S.R. et al. (2012) A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics, 100, 337-344.
-
(2012)
Genomics
, vol.100
, pp. 337-344
-
-
Piccolo, S.R.1
-
19
-
-
84887044836
-
Multiplatform single-sample estimates of transcriptional activation
-
Piccolo,S.R. et al. (2013) Multiplatform single-sample estimates of transcriptional activation. Proc. Natl. Acad. Sci. USA., 110, 17778-17783.
-
(2013)
Proc. Natl. Acad. Sci. USA.
, vol.110
, pp. 17778-17783
-
-
Piccolo, S.R.1
-
20
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan,A.R. and Hall,I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
22
-
-
84920550975
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
-
SEQC/MAQC-III Consortium. (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat. Biotechnol., 32, 903-914.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 903-914
-
-
SEQC/MAQC-III Consortium1
-
23
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth,G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
24
-
-
84866894408
-
Comprehensive genomic characterization of squamous cell lung cancers
-
The Cancer Genome Atlas Research Network. (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature, 489, 519-525.
-
(2012)
Nature
, vol.489
, pp. 519-525
-
-
The Cancer Genome Atlas Research Network1
-
25
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
The Cancer Genome Atlas Research Network et al. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet., 45, 1113-1120.
-
(2013)
Nat. Genet.
, vol.45
, pp. 1113-1120
-
-
The Cancer Genome Atlas Research Network1
-
26
-
-
84905029258
-
Comprehensive molecular profiling of lung adenocarcinoma
-
The Cancer Genome Atlas Research Network. (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature, 511, 543-550.
-
(2014)
Nature
, vol.511
, pp. 543-550
-
-
The Cancer Genome Atlas Research Network1
-
27
-
-
84872033704
-
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
-
Wagner,G.P. et al. (2012) Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theor. Biosci., 131, 281-285.
-
(2012)
Theor. Biosci.
, vol.131
, pp. 281-285
-
-
Wagner, G.P.1
-
28
-
-
78649345104
-
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
-
Wang,K. et al. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, e178.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e178
-
-
Wang, K.1
-
29
-
-
0035949684
-
Predicting the clinical status of human breast cancer by using gene expression profiles
-
West, M. et al. (2001) Predicting the clinical status of human breast cancer by using gene expression profiles. Proc. Natl. Acad. Sci. USA., 98, 11462-11467.
-
(2001)
Proc. Natl. Acad. Sci. USA.
, vol.98
, pp. 11462-11467
-
-
West, M.1
-
30
-
-
84922553800
-
The Cancer Genomics Hub (CGHub): Overcoming cancer through the power of torrential data
-
Wilks,C. et al. (2014) The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database, 2014, 1-10.
-
(2014)
Database
, vol.2014
, pp. 1-10
-
-
Wilks, C.1
-
31
-
-
63849301203
-
The UCSC Cancer Genomics Browser
-
Zhu,J. et al. (2009) The UCSC Cancer Genomics Browser. Nat. Methods, 6, 239-240.
-
(2009)
Nat. Methods
, vol.6
, pp. 239-240
-
-
Zhu, J.1
|