--- a/hicCompareMatrices.xml	Wed Mar 07 04:24:22 2018 -0500
+++ b/hicCompareMatrices.xml	Sat Jun 09 15:23:59 2018 -0400
@@ -1,5 +1,5 @@
 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>normalize and compare two HiC matricies</description>
+    <description>normalize and compare two Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCompareMatrices</token>
         <import>macros.xml</import>
@@ -56,16 +56,43 @@
 
     </tests>
     <help><![CDATA[
-Comparison of HiC matrices
-==========================
-`hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To
-normalize the matrices each element is divided by sum of the matrix.
+Comparison of Hi-C matrices
+===========================
+
+This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To
+normalize the matrices, each element is divided by the sum of the matrix.
+
+**hicCompareMatrices** can be used for example to determine the effect of a mutation compared to wild-type samples on contact enrichment,
+or to see TAD structure modifications near differentially expressed genes between two conditions when followed by ``hicPlotMatrix``.
+It can also be used to compare two biological replicates.
+
+_________________
+
+Usage
+-----
+
+**hicCompareMatrices** is usually perfomed on corrected matrices (``hicCorrectMatrix``) with bins merged (``hicMergeMatrixBins``) depending
+on the downstream analyses to perform (visualisation of a whole chromosome, or of a small region, etc).
 
-Input
------
-- the matricies to be compared
+_________________
+
+Output
+------
+
+Here is an example of a log2ratio comparison between M1BP Knockdown and GST cells in
+*Drosophila melanogaster* on corrected matrices with 50 bins merged (about 30kb bins) plotted using ``hicPlotMatrix``.
 
+.. image:: $PATH_TO_IMAGES/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
+   :width: 50%
 
+In this plot we see that the cells with a M1BP Knockdown display a negative log2ratio compared to the wild-type. Depletion of M1BP thus show a dramatic effect on the distribution of Hi-C contacts in which short range contacts decrease (Ramirez *et al.* 2017,  High-resolution TADs reveal DNA sequences underlying genome organization in flies, https://doi.org/10.1038/s41467-017-02525-w).
+
+Below you can find an example of a log2ratio plot between Hi-C matrices of two biological replicates, no differences are observable which means that the replicates are well correlated.
+
+.. image:: $PATH_TO_IMAGES/hicCompareMatrices_QC_log2_m50_matrix_plot.png
+   :width: 50%
+
+_________________
 
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_