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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedBladderData
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* checking for file ‘curatedBladderData/DESCRIPTION’ ... OK
* preparing ‘curatedBladderData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
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[] \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[]
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[] \T1/zi4/m/n/10 Title: Predictive value of progression-related gene classif
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[] \T1/zi4/m/n/10 Experimenter name: Blaveri E, Simko JP, Korkola JE, Brewer
JL, Baehner F, Mehta K, Devries S, Koppie T, Pejavar S, Carroll P, Waldman FM.
Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[]
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[] \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
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sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[]
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sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[]
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[] \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[]
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
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[] \T1/zi4/m/n/10 Experimenter name: Riester M, Taylor JM, Feifer A, Koppie T
et al. Combination of a novel gene expression signature with a clinical nomogr
am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
Res 2012 Mar 1;18(5):1323-33.[]
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[] \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
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[] \T1/zi4/m/n/10 Experimenter name: Sj?dahl G, Lauss M, L?vgren K, Chebil G
et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 2012 Jun
15;18(12):3377-86.[]
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[] \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[]
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low-ing
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[] \T1/zi4/m/n/10 Experimenter name: Als AB, Dyrskj?t L, von der Maase H, Koe
d K et al. Emmprin and survivin predict response and survival following cisplat
in-containing chemotherapy in patients with advanced bladder cancer. Clin Cance
r Res 2007 Aug 1;13(15 Pt 1):4407-14.[]
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[] \T1/zi4/m/n/10 Title: Emmprin and survivin predict response and survival f
ollowing cisplatin-containing chemotherapy in patients with advanced bladder ca
ncer.[]
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[] \T1/zi4/m/n/10 Experimenter name: Dyrskj?t L, Thykjaer T, Kruh?ffer M, Jen
sen JL et al. Identifying distinct classes of bladder carcinoma using microarra
ys. Nat Genet 2003 Jan;33(1):90-6.[]
[24] [25] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
12.[]
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[] \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
12.[]
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[] \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[]
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Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[]
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sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[]
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sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[]
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[] \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
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am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
Res 2012 Mar 1;18(5):1323-33.[]
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[] \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
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t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[]
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[] \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[]
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Bladder cancer outcome and subtype classification by gene expression.Clin Cance
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[] \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[]
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am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
Res 2012 Mar 1;18(5):1323-33.[]
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[] \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
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linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[]
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ier in primary non-muscle invasive bladder cancer.[]
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[] \T1/zi4/m/n/10 Experimenter name: Blaveri E, Simko JP, Korkola JE, Brewer
JL, Baehner F, Mehta K, Devries S, Koppie T, Pejavar S, Carroll P, Waldman FM.
Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[]
[5] [6]
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[] \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[]
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[] \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures
for molecular grading and outcome.[]
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[] \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[]
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[] \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures
for molecular grading and outcome.[]
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[] \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[]
[13] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/zi4/m/n/10 Experimenter name: Riester M, Taylor JM, Feifer A, Koppie T
et al. Combination of a novel gene expression signature with a clinical nomogr
am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
Res 2012 Mar 1;18(5):1323-33.[]
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[] \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
h a clinical nomogram improves the prediction of survival in high-risk bladder
cancer.[]
[14] [15]
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[] \T1/zi4/m/n/10 Experimenter name: Sj?dahl G, Lauss M, L?vgren K, Chebil G
et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 2012 Jun
15;18(12):3377-86.[]
[18] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
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[] \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[]
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[] \T1/zi4/m/n/10 Title: Transcriptional signatures of Ral GTPase are associa
ted with aggressive clinicopathologic characteristics in human cancer.[]
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[] \T1/ptm/m/it/10 Emm-prin and sur-vivin pre-dict re-sponse and sur-vival fol-
low-ing
[21]
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[] \T1/zi4/m/n/10 Experimenter name: Als AB, Dyrskj?t L, von der Maase H, Koe
d K et al. Emmprin and survivin predict response and survival following cisplat
in-containing chemotherapy in patients with advanced bladder cancer. Clin Cance
r Res 2007 Aug 1;13(15 Pt 1):4407-14.[]
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[] \T1/zi4/m/n/10 Title: Emmprin and survivin predict response and survival f
ollowing cisplatin-containing chemotherapy in patients with advanced bladder ca
ncer.[]
[22] [23] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
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[] \T1/zi4/m/n/10 Experimenter name: Dyrskj?t L, Thykjaer T, Kruh?ffer M, Jen
sen JL et al. Identifying distinct classes of bladder carcinoma using microarra
ys. Nat Genet 2003 Jan;33(1):90-6.[]
[25] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
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[] \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
12.[]
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[] \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
12.[]
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