Mercurial > repos > bgruening > hicexplorer_hicfindtads

annotate hicFindTADs.xml @ 5:db2cc9e1ff76 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:39:05 -0500
parents 8b60271e7e54
children b05f292d220c
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aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>find minimum cuts that correspond to boundaries</description>
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3 <macros>
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4 <token name="@BINARY@">hicFindTADs</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 hicFindTADs
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10 --matrix '$matrix_h5_cooler'
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12 --delta $delta
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13
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14 #if $minBoundaryDistance:
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15 --minBoundaryDistance $minBoundaryDistance
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16 #end if
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17 --minDepth $minDepth
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18 --maxDepth $maxDepth
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19 --step $step
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20 #if $multiple_comparison_conditional.multiple_comparison_selector == 'fdr':
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21 --correctForMultipleTesting fdr
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22 --threshold $multiple_comparison_conditional.threshold
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23 #elif $multiple_comparison_conditional.multiple_comparison_selector == 'bonferroni':
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24 --correctForMultipleTesting bonferroni
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25 --threshold $multiple_comparison_conditional.threshold
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26 #else:
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27 --multipleComparisons None
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28 #end if
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29
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30 --numberOfProcessors @THREADS@
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31 --outPrefix galaxy_tad_prefix
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32 ]]></command>
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33 <inputs>
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34 <expand macro='matrix_h5_cooler_macro' />
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35
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36 <param argument="--minDepth" type="integer" value="40000"
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37 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
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38 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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39 <param argument="--maxDepth" type="integer" value="100000"
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40 label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
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41 help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>
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42 <param argument="--step" type="integer" value="10000"
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43 label="Step size when moving from minDepth to maxDepth"
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44 help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]
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45 until it reaches maxDepth. For example, selecting step=10,000, minDepth=20,000
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46 and maxDepth=150,000 will compute TAD-scores for window sizes:
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47 20,000, 30,000, 40,000, 70,000 and 100,000"/>
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48 <conditional name="multiple_comparison_conditional">
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49 <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections" >
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50 <option value="fdr" selected="True">False discovery rate</option>
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51 <option value="bonferroni">Bonferroni correction</option>
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52 <option value="None">No correction</option>
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53 </param>
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54 <when value="fdr">
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55 <param name="threshold" type="float" value="0.01" label="q-value" />
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56 </when>
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57 <when value="bonferroni">
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58 <param name="threshold" type="float" value="0.01" label="p-value" />
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59 </when>
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60 <when value="None" />
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61 </conditional>
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62 <param argument="--delta" type="float" value="0.001" optional="True"
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63 label="Minimum threshold of the difference between the TAD-separation score of a putative boundary and the mean of the TAD-sep. score of surrounding bins."
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64 help="The delta value reduces spurious boundaries that are shallow, which usually
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65 occur at the center of large TADs when the TAD-sep. score is flat. Higher
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66 delta threshold values produce more conservative boundary estimations. By
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67 default, multiple delta thresholds are saved for the following delta
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68 values: 0.001, 0.01, 0.03, 0.05, 0.1. Other single or multiple values
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69 can be given."/>
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70
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71 <param argument="--minBoundaryDistance" type="integer" value="" optional="True"
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72 label="Minimum distance between boundaries (in bp)."
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73 help="This parameter can be used to reduce spurious boundaries caused by noise. "/>
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74
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75 </inputs>
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76 <outputs>
2
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77
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78 <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed"
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79 label="${tool.name} on ${on_string}: Boundary positions" />
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80
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81 <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph"
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82 label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores" />
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83 <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"
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84 label="${tool.name} on ${on_string}: TAD domains" />
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85 <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"
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86 format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" />
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87
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88 <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm"
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89 format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file" />
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90
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91 <data name="matrix_output" from_work_dir="galaxy_tad_prefix_zscore_matrix.h5"
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92 format="h5" label="${tool.name} on ${on_string}: Z-score matrix in h5" />
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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97
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98 <param name="minDepth" value="60000"/>
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99 <param name="maxDepth" value="180000"/>
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100 <param name="step" value="20000"/>
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101 <param name="minBoundaryDistance" value="20000" />
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102 <conditional name="multiple_comparison_conditional">
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103 <param name="multiple_comparison_selector" value="fdr"/>
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104 <param name="threshold" value="0.1" />
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105 </conditional>
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106 <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" compare="sim_size" delta="35000" />
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107 <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" />
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108 <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" />
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109 <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" />
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110 <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" />
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111 <output name="matrix_output" file="find_TADs/multiFDR_zscore_matrix.h5" ftype="h5" compare="sim_size" delta="50000" />
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115 Calculate TADs
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116 ==============
0
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117
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118 Topological associated domains (TADs) are regions on the DNA which tend to interact within the region a lot, but not outside their boundaries. More information_.
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119
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120 Calculation
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121 ------------
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122 ``hicFindTADs`` computes the TAD regions in two steps: In a first step it computes a TAD-separation score based on a z-score matrix for all bins. The z-score is defined as:
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123
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124 “The absolute value of z represents the distance between the raw score and the population mean in
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125 units of the standard deviation. z is negative when the raw score is below the mean, positive when above.”
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126 [Source_].
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127
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128 .. image:: $PATH_TO_IMAGES/z-score.svg
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129 :width: 100
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130
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131 `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_
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132
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133 In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_.
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134
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135
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136 Input
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137 -----
0
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138
4
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139 Parameters
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140 __________
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141 - contact matrix to compute the TADs on
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142 - minimum window length
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143 - maximum window length
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144 - step size
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145 - multiple testing correction
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146 - minimum threshold
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147 - minimum distance
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148
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149
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150 hicFindTADs tries to identify sensible parameters but those can be change to identify more stringent set of boundaries.
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151
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152 Output
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153 ------
0
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154
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155 - Boundary positions as a bed file
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156 - Matrix with multi-scale TAD scores as a bedgraph
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157 - TAD domains as a bed file
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158 - Boundary information plus score as gff
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159 - TAD information in bm file
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160 - Z-score matrix in h5
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161
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162 The calulated TAD regions can be plotted with ``hicPlotTADs``.
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163
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164
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165 .. image:: $PATH_TO_IMAGES/master_TADs_plot.png
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166 :width: 80 %
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170 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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172 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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173 .. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score
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174 .. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_
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175 ]]></help>
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176 <expand macro="citations" />
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177 </tool>