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author morinlab
date Tue, 06 Dec 2016 20:03:54 -0500
parents 3f5545f5f0c8
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3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <macros>
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2 <xml name="morinlab_citation">
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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4 @unpublished{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8 note = "Unpublished Manuscript",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.},
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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},
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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,
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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
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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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diff changeset
84 Hirst, Martin and Marra, Marco A and Condon, Anne and Aparicio,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
85 Samuel and Shah, Sohrab P",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
86 journal = "Bioinformatics",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
87 volume = 28,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
88 number = 2,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
89 pages = "167--175",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
90 month = "15~" # jan,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
91 year = 2012
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
92 }
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
93 </citation>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
94 </xml>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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95
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diff changeset
96 <xml name="strelka_citation">
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
97 <citation type="bibtex">
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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98 @ARTICLE{Saunders2012-nh,
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99 title = "Strelka: accurate somatic small-variant calling from sequenced
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
100 tumor-normal sample pairs",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
101 author = "Saunders, Christopher T and Wong, Wendy S W and Swamy, Sajani and
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
102 Becq, Jennifer and Murray, Lisa J and Cheetham, R Keira",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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103 journal = "Bioinformatics",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
104 volume = 28,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
105 number = 14,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
106 pages = "1811--1817",
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
107 month = "15~" # jul,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
108 year = 2012
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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109 }
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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110 </citation>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
111 </xml>
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diff changeset
112 <xml name="radia_citation">
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113 <citation type="bibtex">
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114 @article{
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diff changeset
115 Radenbaugh2014-tj,
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116 title={RADIA: RNA and DNA integrated analysis for somatic
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
117 mutation detection},
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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118 author={Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
119 Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
120 David},
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diff changeset
121 journal={PLoS One},
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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122 volume={9},
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
123 number={11},
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124 pages={e111516},
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq 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">
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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",
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135 author = "Ha, Gavin and Roth, Andrew and Khattra, Jaswinder and Ho,
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diff changeset
136 Julie and Yap, Damian and Prentice, Leah M and Melnyk,
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137 Nataliya and McPherson, Andrew and Bashashati, Ali and Laks,
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138 Emma and Biele, Justina and Ding, Jiarui and Le, Alan and
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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
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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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diff changeset
144 volume = 24,
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diff changeset
145 number = 11,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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146 pages = "1881--1893",
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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 }
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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151 </citation>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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152 </xml>
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153 </macros>