PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Identifieur interne : 000670 ( Main/Exploration ); précédent : 000669; suivant : 000671PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Auteurs : Xin Feng [États-Unis, Canada] ; Robert Grossman [États-Unis] ; Lincoln Stein [États-Unis, Canada]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2011.
Abstract
Chromatin immunoprecipitation (ChIP), coupled with massively parallel short-read sequencing (seq) is used to probe chromatin dynamics. Although there are many algorithms to call peaks from ChIP-seq datasets, most are tuned either to handle punctate sites, such as transcriptional factor binding sites, or broad regions, such as histone modification marks; few can do both. Other algorithms are limited in their configurability, performance on large data sets, and ability to distinguish closely-spaced peaks.
In this paper, we introduce PeakRanger, a peak caller software package that works equally well on punctate and broad sites, can resolve closely-spaced peaks, has excellent performance, and is easily customized. In addition, PeakRanger can be run in a parallel cloud computing environment to obtain extremely high performance on very large data sets. We present a series of benchmarks to evaluate PeakRanger against 10 other peak callers, and demonstrate the performance of PeakRanger on both real and synthetic data sets. We also present real world usages of PeakRanger, including peak-calling in the modENCODE project.
Compared to other peak callers tested, PeakRanger offers improved resolution in distinguishing extremely closely-spaced peaks. PeakRanger has above-average spatial accuracy in terms of identifying the precise location of binding events. PeakRanger also has excellent sensitivity and specificity in all benchmarks evaluated. In addition, PeakRanger offers significant improvements in run time when running on a single processor system, and very marked improvements when allowed to take advantage of the MapReduce parallel environment offered by a cloud computing resource. PeakRanger can be downloaded at the official site of modENCODE project:
Url:
DOI: 10.1186/1471-2105-12-139
PubMed: 21554709
PubMed Central: 3103446
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000278
- to stream Pmc, to step Curation: 000278
- to stream Pmc, to step Checkpoint: 000488
- to stream Ncbi, to step Merge: 000228
- to stream Ncbi, to step Curation: 000228
- to stream Ncbi, to step Checkpoint: 000228
- to stream Main, to step Merge: 000672
- to stream Main, to step Curation: 000670
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">PeakRanger: A cloud-enabled peak caller for ChIP-seq data</title><author><name sortKey="Feng, Xin" sort="Feng, Xin" uniqKey="Feng X" first="Xin" last="Feng">Xin Feng</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3</wicri:regionArea><wicri:noRegion>ON M5G 0A3</wicri:noRegion></affiliation></author><author><name sortKey="Grossman, Robert" sort="Grossman, Robert" uniqKey="Grossman R" first="Robert" last="Grossman">Robert Grossman</name><affiliation wicri:level="2"><nlm:aff id="I4">Institute for Genomics & Systems Biology, The University of Chicago, Cummings Life Sciences Center 431A, 920 East 58th Street, Chicago, IL 60637, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Genomics & Systems Biology, The University of Chicago, Cummings Life Sciences Center 431A, 920 East 58th Street, Chicago, IL 60637</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3</wicri:regionArea><wicri:noRegion>ON M5G 0A3</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21554709</idno><idno type="pmc">3103446</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103446</idno><idno type="RBID">PMC:3103446</idno><idno type="doi">10.1186/1471-2105-12-139</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000278</idno><idno type="wicri:Area/Pmc/Curation">000278</idno><idno type="wicri:Area/Pmc/Checkpoint">000488</idno><idno type="wicri:Area/Ncbi/Merge">000228</idno><idno type="wicri:Area/Ncbi/Curation">000228</idno><idno type="wicri:Area/Ncbi/Checkpoint">000228</idno><idno type="wicri:Area/Main/Merge">000672</idno><idno type="wicri:Area/Main/Curation">000670</idno><idno type="wicri:Area/Main/Exploration">000670</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">PeakRanger: A cloud-enabled peak caller for ChIP-seq data</title><author><name sortKey="Feng, Xin" sort="Feng, Xin" uniqKey="Feng X" first="Xin" last="Feng">Xin Feng</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3</wicri:regionArea><wicri:noRegion>ON M5G 0A3</wicri:noRegion></affiliation></author><author><name sortKey="Grossman, Robert" sort="Grossman, Robert" uniqKey="Grossman R" first="Robert" last="Grossman">Robert Grossman</name><affiliation wicri:level="2"><nlm:aff id="I4">Institute for Genomics & Systems Biology, The University of Chicago, Cummings Life Sciences Center 431A, 920 East 58th Street, Chicago, IL 60637, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Genomics & Systems Biology, The University of Chicago, Cummings Life Sciences Center 431A, 920 East 58th Street, Chicago, IL 60637</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3</wicri:regionArea><wicri:noRegion>ON M5G 0A3</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Chromatin immunoprecipitation (ChIP), coupled with massively parallel short-read sequencing (seq) is used to probe chromatin dynamics. Although there are many algorithms to call peaks from ChIP-seq datasets, most are tuned either to handle punctate sites, such as transcriptional factor binding sites, or broad regions, such as histone modification marks; few can do both. Other algorithms are limited in their configurability, performance on large data sets, and ability to distinguish closely-spaced peaks.</p></sec><sec><title>Results</title><p>In this paper, we introduce PeakRanger, a peak caller software package that works equally well on punctate and broad sites, can resolve closely-spaced peaks, has excellent performance, and is easily customized. In addition, PeakRanger can be run in a parallel cloud computing environment to obtain extremely high performance on very large data sets. We present a series of benchmarks to evaluate PeakRanger against 10 other peak callers, and demonstrate the performance of PeakRanger on both real and synthetic data sets. We also present real world usages of PeakRanger, including peak-calling in the modENCODE project.</p></sec><sec><title>Conclusions</title><p>Compared to other peak callers tested, PeakRanger offers improved resolution in distinguishing extremely closely-spaced peaks. PeakRanger has above-average spatial accuracy in terms of identifying the precise location of binding events. PeakRanger also has excellent sensitivity and specificity in all benchmarks evaluated. In addition, PeakRanger offers significant improvements in run time when running on a single processor system, and very marked improvements when allowed to take advantage of the MapReduce parallel environment offered by a cloud computing resource. PeakRanger can be downloaded at the official site of modENCODE project: <ext-link ext-link-type="uri" xlink:href="http://www.modencode.org/software/ranger/">http://www.modencode.org/software/ranger/</ext-link></p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Mikkelsen, Ts" uniqKey="Mikkelsen T">TS Mikkelsen</name></author><author><name sortKey="Ku, M" uniqKey="Ku M">M Ku</name></author><author><name sortKey="Jaffe, Db" uniqKey="Jaffe D">DB Jaffe</name></author><author><name sortKey="Issac, B" uniqKey="Issac B">B Issac</name></author><author><name sortKey="Lieberman, E" uniqKey="Lieberman E">E Lieberman</name></author><author><name sortKey="Giannoukos, G" uniqKey="Giannoukos G">G Giannoukos</name></author><author><name sortKey="Alvarez, P" uniqKey="Alvarez P">P Alvarez</name></author><author><name sortKey="Brockman, W" uniqKey="Brockman W">W Brockman</name></author><author><name sortKey="Kim, Tk" uniqKey="Kim T">TK Kim</name></author><author><name sortKey="Koche, Rp" uniqKey="Koche R">RP Koche</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name></author><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author><author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name></author><author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robertson, G" uniqKey="Robertson G">G Robertson</name></author><author><name sortKey="Hirst, M" uniqKey="Hirst M">M Hirst</name></author><author><name sortKey="Bainbridge, M" uniqKey="Bainbridge M">M Bainbridge</name></author><author><name sortKey="Bilenky, M" uniqKey="Bilenky M">M Bilenky</name></author><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name></author><author><name sortKey="Zeng, T" uniqKey="Zeng T">T Zeng</name></author><author><name sortKey="Euskirchen, G" uniqKey="Euskirchen G">G Euskirchen</name></author><author><name sortKey="Bernier, B" uniqKey="Bernier B">B Bernier</name></author><author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name></author><author><name sortKey="Delaney, A" uniqKey="Delaney A">A Delaney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name></author><author><name sortKey="Cuddapah, S" uniqKey="Cuddapah S">S Cuddapah</name></author><author><name sortKey="Cui, K" uniqKey="Cui K">K Cui</name></author><author><name sortKey="Roh, Ty" uniqKey="Roh T">TY Roh</name></author><author><name sortKey="Schones, De" uniqKey="Schones D">DE Schones</name></author><author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name></author><author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name></author><author><name sortKey="Chepelev, I" uniqKey="Chepelev I">I Chepelev</name></author><author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Park, Pj" uniqKey="Park P">PJ Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ren, B" uniqKey="Ren B">B Ren</name></author><author><name sortKey="Robert, F" uniqKey="Robert F">F Robert</name></author><author><name sortKey="Wyrick, Jj" uniqKey="Wyrick J">JJ Wyrick</name></author><author><name sortKey="Aparicio, O" uniqKey="Aparicio O">O Aparicio</name></author><author><name sortKey="Jennings, Eg" uniqKey="Jennings E">EG Jennings</name></author><author><name sortKey="Simon, I" uniqKey="Simon I">I Simon</name></author><author><name sortKey="Zeitlinger, J" uniqKey="Zeitlinger J">J Zeitlinger</name></author><author><name sortKey="Schreiber, J" uniqKey="Schreiber J">J Schreiber</name></author><author><name sortKey="Hannett, N" uniqKey="Hannett N">N Hannett</name></author><author><name sortKey="Kanin, E" uniqKey="Kanin E">E Kanin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Iyer, Vr" uniqKey="Iyer V">VR Iyer</name></author><author><name sortKey="Horak, Ce" uniqKey="Horak C">CE Horak</name></author><author><name sortKey="Scafe, Cs" uniqKey="Scafe C">CS Scafe</name></author><author><name sortKey="Botstein, D" uniqKey="Botstein D">D Botstein</name></author><author><name sortKey="Snyder, M" uniqKey="Snyder M">M Snyder</name></author><author><name sortKey="Brown, Po" uniqKey="Brown P">PO Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pepke, S" uniqKey="Pepke S">S Pepke</name></author><author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name></author><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lun, D" uniqKey="Lun D">D Lun</name></author><author><name sortKey="Sherrid, A" uniqKey="Sherrid A">A Sherrid</name></author><author><name sortKey="Weiner, B" uniqKey="Weiner B">B Weiner</name></author><author><name sortKey="Sherman, D" uniqKey="Sherman D">D Sherman</name></author><author><name sortKey="Galagan, J" uniqKey="Galagan J">J Galagan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blahnik, Kr" uniqKey="Blahnik K">KR Blahnik</name></author><author><name sortKey="Dou, L" uniqKey="Dou L">L Dou</name></author><author><name sortKey="O Geen, H" uniqKey="O Geen H">H O'Geen</name></author><author><name sortKey="Mcphillips, T" uniqKey="Mcphillips T">T McPhillips</name></author><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name></author><author><name sortKey="Cao, Ar" uniqKey="Cao A">AR Cao</name></author><author><name sortKey="Iyengar, S" uniqKey="Iyengar S">S Iyengar</name></author><author><name sortKey="Nicolet, Cm" uniqKey="Nicolet C">CM Nicolet</name></author><author><name sortKey="Lud Scher, B" uniqKey="Lud Scher B">B Ludäscher</name></author><author><name sortKey="Korf, I" uniqKey="Korf I">I Korf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ji, H" uniqKey="Ji H">H Ji</name></author><author><name sortKey="Jiang, H" uniqKey="Jiang H">H Jiang</name></author><author><name sortKey="Ma, W" uniqKey="Ma W">W Ma</name></author><author><name sortKey="Johnson, D" uniqKey="Johnson D">D Johnson</name></author><author><name sortKey="Myers, R" uniqKey="Myers R">R Myers</name></author><author><name sortKey="Wong, W" uniqKey="Wong W">W Wong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jothi, R" uniqKey="Jothi R">R Jothi</name></author><author><name sortKey="Cuddapah, S" uniqKey="Cuddapah S">S Cuddapah</name></author><author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name></author><author><name sortKey="Cui, K" uniqKey="Cui K">K Cui</name></author><author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zang, Cz" uniqKey="Zang C">CZ Zang</name></author><author><name sortKey="Schones, De" uniqKey="Schones D">DE Schones</name></author><author><name sortKey="Zeng, C" uniqKey="Zeng C">C Zeng</name></author><author><name sortKey="Cui, Kr" uniqKey="Cui K">KR Cui</name></author><author><name sortKey="Zhao, Kj" uniqKey="Zhao K">KJ Zhao</name></author><author><name sortKey="Peng, Wq" uniqKey="Peng W">WQ Peng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fejes, A" uniqKey="Fejes A">A Fejes</name></author><author><name sortKey="Robertson, G" uniqKey="Robertson G">G Robertson</name></author><author><name sortKey="Bilenky, M" uniqKey="Bilenky M">M Bilenky</name></author><author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name></author><author><name sortKey="Bainbridge, M" uniqKey="Bainbridge M">M Bainbridge</name></author><author><name sortKey="Jones, S" uniqKey="Jones S">S Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boyle, Ap" uniqKey="Boyle A">AP Boyle</name></author><author><name sortKey="Guinney, J" uniqKey="Guinney J">J Guinney</name></author><author><name sortKey="Crawford, Ge" uniqKey="Crawford G">GE Crawford</name></author><author><name sortKey="Furey, Ts" uniqKey="Furey T">TS Furey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuteja, G" uniqKey="Tuteja G">G Tuteja</name></author><author><name sortKey="White, P" uniqKey="White P">P White</name></author><author><name sortKey="Schug, J" uniqKey="Schug J">J Schug</name></author><author><name sortKey="Kaestner, Kh" uniqKey="Kaestner K">KH Kaestner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name></author><author><name sortKey="Meyer, C" uniqKey="Meyer C">C Meyer</name></author><author><name sortKey="Eeckhoute, J" uniqKey="Eeckhoute J">J Eeckhoute</name></author><author><name sortKey="Johnson, D" uniqKey="Johnson D">D Johnson</name></author><author><name sortKey="Bernstein, B" uniqKey="Bernstein B">B Bernstein</name></author><author><name sortKey="Nussbaum, C" uniqKey="Nussbaum C">C Nussbaum</name></author><author><name sortKey="Myers, R" uniqKey="Myers R">R Myers</name></author><author><name sortKey="Brown, M" uniqKey="Brown M">M Brown</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rozowsky, J" uniqKey="Rozowsky J">J Rozowsky</name></author><author><name sortKey="Euskirchen, G" uniqKey="Euskirchen G">G Euskirchen</name></author><author><name sortKey="Auerbach, R" uniqKey="Auerbach R">R Auerbach</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Gibson, T" uniqKey="Gibson T">T Gibson</name></author><author><name sortKey="Bjornson, R" uniqKey="Bjornson R">R Bjornson</name></author><author><name sortKey="Carriero, N" uniqKey="Carriero N">N Carriero</name></author><author><name sortKey="Snyder, M" uniqKey="Snyder M">M Snyder</name></author><author><name sortKey="Gerstein, M" uniqKey="Gerstein M">M Gerstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Valouev, A" uniqKey="Valouev A">A Valouev</name></author><author><name sortKey="Johnson, D" uniqKey="Johnson D">D Johnson</name></author><author><name sortKey="Sundquist, A" uniqKey="Sundquist A">A Sundquist</name></author><author><name sortKey="Medina, C" uniqKey="Medina C">C Medina</name></author><author><name sortKey="Anton, E" uniqKey="Anton E">E Anton</name></author><author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name></author><author><name sortKey="Myers, R" uniqKey="Myers R">R Myers</name></author><author><name sortKey="Sidow, A" uniqKey="Sidow A">A Sidow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kharchenko, P" uniqKey="Kharchenko P">P Kharchenko</name></author><author><name sortKey="Tolstorukov, M" uniqKey="Tolstorukov M">M Tolstorukov</name></author><author><name sortKey="Park, P" uniqKey="Park P">P Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nix, D" uniqKey="Nix D">D Nix</name></author><author><name sortKey="Courdy, S" uniqKey="Courdy S">S Courdy</name></author><author><name sortKey="Boucher, K" uniqKey="Boucher K">K Boucher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guo, Y" uniqKey="Guo Y">Y Guo</name></author><author><name sortKey="Papachristoudis, G" uniqKey="Papachristoudis G">G Papachristoudis</name></author><author><name sortKey="Altshuler, Rc" uniqKey="Altshuler R">RC Altshuler</name></author><author><name sortKey="Gerber, Gk" uniqKey="Gerber G">GK Gerber</name></author><author><name sortKey="Jaakkola, Ts" uniqKey="Jaakkola T">TS Jaakkola</name></author><author><name sortKey="Gifford, Dk" uniqKey="Gifford D">DK Gifford</name></author><author><name sortKey="Mahony, S" uniqKey="Mahony S">S Mahony</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author><author><name sortKey="Williams, Ba" uniqKey="Williams B">BA Williams</name></author><author><name sortKey="Mccue, K" uniqKey="Mccue K">K McCue</name></author><author><name sortKey="Schaeffer, L" uniqKey="Schaeffer L">L Schaeffer</name></author><author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, Z" uniqKey="Qin Z">Z Qin</name></author><author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name></author><author><name sortKey="Shen, J" uniqKey="Shen J">J Shen</name></author><author><name sortKey="Maher, C" uniqKey="Maher C">C Maher</name></author><author><name sortKey="Hu, M" uniqKey="Hu M">M Hu</name></author><author><name sortKey="Kalyana Sundaram, S" uniqKey="Kalyana Sundaram S">S Kalyana-Sundaram</name></author><author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name></author><author><name sortKey="Chinnaiyan, A" uniqKey="Chinnaiyan A">A Chinnaiyan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilbanks, Eg" uniqKey="Wilbanks E">EG Wilbanks</name></author><author><name sortKey="Facciotti, Mt" uniqKey="Facciotti M">MT Facciotti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name></author><author><name sortKey="Gribskov, M" uniqKey="Gribskov M">M Gribskov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Celniker, Se" uniqKey="Celniker S">SE Celniker</name></author><author><name sortKey="Dillon, Lal" uniqKey="Dillon L">LAL Dillon</name></author><author><name sortKey="Gerstein, Mb" uniqKey="Gerstein M">MB Gerstein</name></author><author><name sortKey="Gunsalus, Kc" uniqKey="Gunsalus K">KC Gunsalus</name></author><author><name sortKey="Henikoff, S" uniqKey="Henikoff S">S Henikoff</name></author><author><name sortKey="Karpen, Gh" uniqKey="Karpen G">GH Karpen</name></author><author><name sortKey="Kellis, M" uniqKey="Kellis M">M Kellis</name></author><author><name sortKey="Lai, Ec" uniqKey="Lai E">EC Lai</name></author><author><name sortKey="Lieb, Jd" uniqKey="Lieb J">JD Lieb</name></author><author><name sortKey="Macalpine, Dm" uniqKey="Macalpine D">DM MacAlpine</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name></author><author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name></author><author><name sortKey="Salzberg, S" uniqKey="Salzberg S">S Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Handsaker, B" uniqKey="Handsaker B">B Handsaker</name></author><author><name sortKey="Wysoker, A" uniqKey="Wysoker A">A Wysoker</name></author><author><name sortKey="Fennell, T" uniqKey="Fennell T">T Fennell</name></author><author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name></author><author><name sortKey="Homer, N" uniqKey="Homer N">N Homer</name></author><author><name sortKey="Marth, G" uniqKey="Marth G">G Marth</name></author><author><name sortKey="Abecasis, G" uniqKey="Abecasis G">G Abecasis</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stein, L" uniqKey="Stein L">L Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Armbrust, M" uniqKey="Armbrust M">M Armbrust</name></author><author><name sortKey="Fox, A" uniqKey="Fox A">A Fox</name></author><author><name sortKey="Griffith, R" uniqKey="Griffith R">R Griffith</name></author><author><name sortKey="Joseph, Ad" uniqKey="Joseph A">AD Joseph</name></author><author><name sortKey="Katz, Rh" uniqKey="Katz R">RH Katz</name></author><author><name sortKey="Konwinski, A" uniqKey="Konwinski A">A Konwinski</name></author><author><name sortKey="Lee, G" uniqKey="Lee G">G Lee</name></author><author><name sortKey="Patterson, Da" uniqKey="Patterson D">DA Patterson</name></author><author><name sortKey="Rabkin, A" uniqKey="Rabkin A">A Rabkin</name></author><author><name sortKey="Stoica, I" uniqKey="Stoica I">I Stoica</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jeffrey Dean, Sg" uniqKey="Jeffrey Dean S">SG Jeffrey Dean</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="He, Hh" uniqKey="He H">HH He</name></author><author><name sortKey="Meyer, Ca" uniqKey="Meyer C">CA Meyer</name></author><author><name sortKey="Shin, H" uniqKey="Shin H">H Shin</name></author><author><name sortKey="Bailey, St" uniqKey="Bailey S">ST Bailey</name></author><author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name></author><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q Wang</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Xu, K" uniqKey="Xu K">K Xu</name></author><author><name sortKey="Ni, M" uniqKey="Ni M">M Ni</name></author><author><name sortKey="Lupien, M" uniqKey="Lupien M">M Lupien</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heintzman, Nd" uniqKey="Heintzman N">ND Heintzman</name></author><author><name sortKey="Hon, Gc" uniqKey="Hon G">GC Hon</name></author><author><name sortKey="Hawkins, Rd" uniqKey="Hawkins R">RD Hawkins</name></author><author><name sortKey="Kheradpour, P" uniqKey="Kheradpour P">P Kheradpour</name></author><author><name sortKey="Stark, A" uniqKey="Stark A">A Stark</name></author><author><name sortKey="Harp, Lf" uniqKey="Harp L">LF Harp</name></author><author><name sortKey="Ye, Z" uniqKey="Ye Z">Z Ye</name></author><author><name sortKey="Lee, Lk" uniqKey="Lee L">LK Lee</name></author><author><name sortKey="Stuart, Rk" uniqKey="Stuart R">RK Stuart</name></author><author><name sortKey="Ching, Cw" uniqKey="Ching C">CW Ching</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ramsey, Sa" uniqKey="Ramsey S">SA Ramsey</name></author><author><name sortKey="Knijnenburg, Ta" uniqKey="Knijnenburg T">TA Knijnenburg</name></author><author><name sortKey="Kennedy, Ka" uniqKey="Kennedy K">KA Kennedy</name></author><author><name sortKey="Zak, De" uniqKey="Zak D">DE Zak</name></author><author><name sortKey="Gilchrist, M" uniqKey="Gilchrist M">M Gilchrist</name></author><author><name sortKey="Gold, Es" uniqKey="Gold E">ES Gold</name></author><author><name sortKey="Johnson, Cd" uniqKey="Johnson C">CD Johnson</name></author><author><name sortKey="Lampano, Ae" uniqKey="Lampano A">AE Lampano</name></author><author><name sortKey="Litvak, V" uniqKey="Litvak V">V Litvak</name></author><author><name sortKey="Navarro, G" uniqKey="Navarro G">G Navarro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gerstein, Mb" uniqKey="Gerstein M">MB Gerstein</name></author><author><name sortKey="Lu, Zj" uniqKey="Lu Z">ZJ Lu</name></author><author><name sortKey="Van Nostrand, El" uniqKey="Van Nostrand E">EL Van Nostrand</name></author><author><name sortKey="Cheng, C" uniqKey="Cheng C">C Cheng</name></author><author><name sortKey="Arshinoff, Bi" uniqKey="Arshinoff B">BI Arshinoff</name></author><author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name></author><author><name sortKey="Yip, Ky" uniqKey="Yip K">KY Yip</name></author><author><name sortKey="Robilotto, R" uniqKey="Robilotto R">R Robilotto</name></author><author><name sortKey="Rechtsteiner, A" uniqKey="Rechtsteiner A">A Rechtsteiner</name></author><author><name sortKey="Ikegami, K" uniqKey="Ikegami K">K Ikegami</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li><li>États-Unis</li></country><region><li>Illinois</li><li>État de New York</li></region></list><tree><country name="États-Unis"><region name="État de New York"><name sortKey="Feng, Xin" sort="Feng, Xin" uniqKey="Feng X" first="Xin" last="Feng">Xin Feng</name></region><name sortKey="Feng, Xin" sort="Feng, Xin" uniqKey="Feng X" first="Xin" last="Feng">Xin Feng</name><name sortKey="Grossman, Robert" sort="Grossman, Robert" uniqKey="Grossman R" first="Robert" last="Grossman">Robert Grossman</name><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name></country><country name="Canada"><noRegion><name sortKey="Feng, Xin" sort="Feng, Xin" uniqKey="Feng X" first="Xin" last="Feng">Xin Feng</name></noRegion><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000670 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000670 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3103446
|texte= PeakRanger: A cloud-enabled peak caller for ChIP-seq data
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21554709" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |