Mercurial > repos > morinlab > delly

annotate citations.xml @ 0:e3b753e2ee24 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/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:20:05 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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1 <macros>
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2 <xml name="morinlab_citation">
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly 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4 @unpublished{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8 note = "Unpublished Manuscript",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.},
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly 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},
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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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84 Hirst, Martin and Marra, Marco A and Condon, Anne and Aparicio,
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diff changeset
85 Samuel and Shah, Sohrab P",
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morinlab
parents:
diff changeset
86 journal = "Bioinformatics",
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
87 volume = 28,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
88 number = 2,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
89 pages = "167--175",
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
90 month = "15~" # jan,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
91 year = 2012
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
92 }
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
93 </citation>
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
94 </xml>
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
95
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
96 <xml name="strelka_citation">
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
97 <citation type="bibtex">
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
98 @ARTICLE{Saunders2012-nh,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
99 title = "Strelka: accurate somatic small-variant calling from sequenced
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
100 tumor-normal sample pairs",
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
101 author = "Saunders, Christopher T and Wong, Wendy S W and Swamy, Sajani and
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
102 Becq, Jennifer and Murray, Lisa J and Cheetham, R Keira",
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
103 journal = "Bioinformatics",
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
104 volume = 28,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
105 number = 14,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
106 pages = "1811--1817",
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
107 month = "15~" # jul,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
108 year = 2012
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
109 }
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
110 </citation>
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
111 </xml>
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
112 <xml name="radia_citation">
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
113 <citation type="bibtex">
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morinlab
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diff changeset
114 @article{
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
115 Radenbaugh2014-tj,
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morinlab
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diff changeset
116 title={RADIA: RNA and DNA integrated analysis for somatic
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
117 mutation detection},
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diff changeset
118 author={Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
119 Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
120 David},
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morinlab
parents:
diff changeset
121 journal={PLoS One},
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morinlab
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diff changeset
122 volume={9},
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diff changeset
123 number={11},
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morinlab
parents:
diff changeset
124 pages={e111516},
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diff changeset
125 year={2014},
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diff changeset
126 publisher={PLoS}
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diff changeset
127 }
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diff changeset
128 </citation>
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diff changeset
129 </xml>
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diff changeset
130 <xml name="titan_citation">
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diff changeset
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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diff changeset
134 populations from tumor whole-genome sequence data",
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diff changeset
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,
e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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diff changeset
137 Nataliya and McPherson, Andrew and Bashashati, Ali and Laks,
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diff changeset
138 Emma and Biele, Justina and Ding, Jiarui and Le, Alan and
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diff changeset
139 Rosner, Jamie and Shumansky, Karey and Marra, Marco A and
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morinlab
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diff changeset
140 Gilks, C Blake and Huntsman, David G and McAlpine, Jessica N
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morinlab
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diff changeset
141 and Aparicio, Samuel and Shah, Sohrab P",
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diff changeset
142 journal = "Genome Res.",
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143 publisher = "Cold Spring Harbor Lab",
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morinlab
parents:
diff changeset
144 volume = 24,
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parents:
diff changeset
145 number = 11,
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morinlab
parents:
diff changeset
146 pages = "1881--1893",
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diff changeset
147 month = "1~" # nov,
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diff changeset
148 year = 2014,
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149 keywords = "computational method"
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150 }
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diff changeset
151 </citation>
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152 </xml>
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153 </macros>