Mercurial > repos > morinlab > vardictjava

annotate citations.xml @ 0:fba18d3160d1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:37:45 -0400
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fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <macros>
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2 <xml name="morinlab_citation">
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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3 <citation type="bibtex">
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4 @unpublished{
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5 albuquerque2016galaxy,
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6 author = "Marco Albuquerque and Bruno Grande and Elie Ritch and Martin Krzywinski and Prasath Pararajalingam and Selin Jessa and Paul Boutros and Sohrab Shah and Ryan Morin",
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7 title = "A Suite of Galaxy Tools for Cancer Mutational Analysis",
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8 note = "Unpublished Manuscript",
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9 year = "2016"
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10 }
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11 </citation>
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12 </xml>
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13 <xml name="vardict_citation">
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14 <citation type="bibtex">
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15 @article{
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16 Lai20062016,
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17 title = {VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research},
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18 author = {Lai, Zhongwu and Markovets, Aleksandra and Ahdesmaki, Miika and Chapman, Brad and Hofmann, Oliver and McEwen, Robert and Johnson, Justin and Dougherty, Brian and Barrett, J. Carl and Dry, Jonathan R.},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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19 journal = {Nucleic Acids Research}
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20 volume = {44},
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21 number = {11},
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22 pages = {e108},
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23 year = {2016},
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24 doi = {10.1093/nar/gkw227}
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25 }
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26 </citation>
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27 </xml>
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28 <xml name="somatic_sniper_citation">
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29 <citation>
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30 @article{
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31 Larson01022012,
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32 author = {Larson, David E. and Harris, Christopher C. and Chen, Ken and Koboldt, Daniel C. and Abbott, Travis E. and Dooling, David J. and Ley, Timothy J. and Mardis, Elaine R. and Wilson, Richard K. and Ding, Li},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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33 title = {SomaticSniper: identification of somatic point mutations in whole genome sequencing data},
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34 volume = {28},
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35 number = {3},
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36 pages = {311-317},
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37 year = {2012},
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38 doi = {10.1093/bioinformatics/btr665},
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39 journal = {Bioinformatics}
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40 }
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41 </citation>
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42 </xml>
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43 <xml name="galaxy_citation">
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44 <citation>
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45 @ARTICLE{Goecks2010-ra,
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46 title = "Galaxy: a comprehensive approach for supporting accessible,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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47 reproducible, and transparent computational research in the life
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48 sciences",
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49 author = "Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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50 {Galaxy Team}",
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51 journal = "Genome Biol.",
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52 volume = 11,
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53 number = 8,
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54 pages = "R86",
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55 month = "25~",
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56 year = 2010
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57 }
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58 </citation>
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59 </xml>
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60
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61 <xml name="delly_citation">
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62 <citation>
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63 @ARTICLE{Rausch2012-yi,
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64 title = "{DELLY}: structural variant discovery by integrated paired-end
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65 and split-read analysis",
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66 author = "Rausch, Tobias and Zichner, Thomas and Schlattl, Andreas and
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67 St{\"{u}}tz, Adrian M and Benes, Vladimir and Korbel, Jan O",
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68 journal = "Bioinformatics",
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69 volume = 28,
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70 number = 18,
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71 pages = "i333--i339",
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72 month = "15~",
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73 year = 2012
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74 }
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75 </citation>
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76 </xml>
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77 <xml name="mutationseq_citation">
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78 <citation type="bibtex">
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79 @ARTICLE{Ding2012-jq,
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80 title = "Feature-based classifiers for somatic mutation detection in
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81 tumour-normal paired sequencing data",
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82 author = "Ding, Jiarui and Bashashati, Ali and Roth, Andrew and Oloumi,
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83 Arusha and Tse, Kane and Zeng, Thomas and Haffari, Gholamreza and
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84 Hirst, Martin and Marra, Marco A and Condon, Anne and Aparicio,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
85 Samuel and Shah, Sohrab P",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
86 journal = "Bioinformatics",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
87 volume = 28,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
88 number = 2,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
89 pages = "167--175",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
90 month = "15~" # jan,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
91 year = 2012
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
92 }
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
93 </citation>
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
94 </xml>
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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95
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
96 <xml name="strelka_citation">
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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parents:
diff changeset
97 <citation type="bibtex">
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
98 @ARTICLE{Saunders2012-nh,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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99 title = "Strelka: accurate somatic small-variant calling from sequenced
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
100 tumor-normal sample pairs",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
101 author = "Saunders, Christopher T and Wong, Wendy S W and Swamy, Sajani and
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
102 Becq, Jennifer and Murray, Lisa J and Cheetham, R Keira",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
103 journal = "Bioinformatics",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
104 volume = 28,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
105 number = 14,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
106 pages = "1811--1817",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
107 month = "15~" # jul,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
108 year = 2012
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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109 }
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
110 </citation>
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
111 </xml>
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
112 <xml name="radia_citation">
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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113 <citation type="bibtex">
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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114 @article{
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
115 Radenbaugh2014-tj,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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116 title={RADIA: RNA and DNA integrated analysis for somatic
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
117 mutation detection},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
118 author={Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
119 Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
120 David},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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parents:
diff changeset
121 journal={PLoS One},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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122 volume={9},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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123 number={11},
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124 pages={e111516},
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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125 year={2014},
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126 publisher={PLoS}
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127 }
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128 </citation>
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129 </xml>
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130 <xml name="titan_citation">
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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131 <citation type="bibtex">
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132 @ARTICLE{Ha2014-pu,
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133 title = "{TITAN}: inference of copy number architectures in clonal cell
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134 populations from tumor whole-genome sequence data",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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135 author = "Ha, Gavin and Roth, Andrew and Khattra, Jaswinder and Ho,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
136 Julie and Yap, Damian and Prentice, Leah M and Melnyk,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
137 Nataliya and McPherson, Andrew and Bashashati, Ali and Laks,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
138 Emma and Biele, Justina and Ding, Jiarui and Le, Alan and
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
139 Rosner, Jamie and Shumansky, Karey and Marra, Marco A and
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diff changeset
140 Gilks, C Blake and Huntsman, David G and McAlpine, Jessica N
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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141 and Aparicio, Samuel and Shah, Sohrab P",
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142 journal = "Genome Res.",
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143 publisher = "Cold Spring Harbor Lab",
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morinlab
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144 volume = 24,
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145 number = 11,
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
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146 pages = "1881--1893",
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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147 month = "1~" # nov,
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148 year = 2014,
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149 keywords = "computational method"
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150 }
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151 </citation>
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152 </xml>
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153 </macros>