comparison computeMatrix.xml @ 43:c5787c91cab8 draft

Uploaded

42:ef1232cedacb

<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.3">
    <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">computeMatrix</token>

    </tests>
  <help>

**What it does**

This tool summarizes and prepares an intermediary file
containing scores associated with genomic regions that can be used
afterwards to plot a heatmap or a profile.

Genomic regions can really be anything - genes, parts of genes, ChIP-seq
peaks, favorite genome regions... as long as you provide a proper file
in BED or INTERVAL format. This tool can also be used to filter and sort
regions according to their score.


.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
   :alt: Relationship between computeMatrix, heatmapper and profiler


You can find more details in the `computeMatrix wiki`_.

.. _computeMatrix wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix


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@REFERENCES@

43:c5787c91cab8

<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.4">
    <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">computeMatrix</token>

    </tests>
  <help>

**What it does**

This tool prepares an intermediary file (a gzipped table of values)
that contains scores associated with genomic regions that can be used
afterwards to plot a heatmap or a profile.

Genomic regions can really be anything - genes, parts of genes, ChIP-seq
peaks, favorite genome regions... as long as you provide a proper file
in BED or INTERVAL format. If you would like to compare different groups of regions
(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.

computeMatrix can also be used to filter and sort
regions according to their score by making use of its advanced output options.


.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
   :alt: Relationship between computeMatrix, heatmapper and profiler


You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix


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@REFERENCES@