Mercurial > repos > bgruening > deeptools

comparison computeMatrix.xml @ 24:d7c9fd76e41e draft

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author bgruening
date Tue, 04 Feb 2014 09:12:07 -0500
parents 8c452f37c896
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23:8c452f37c896 24:d7c9fd76e41e
192 </tests> 192 </tests>
193 <help> 193 <help>
194 194
195 **What it does** 195 **What it does**
196 196
197 This tool summarizes and prepares an intermediary file 197 This tool prepares an intermediary file (a gzipped table of values)
198 containing scores associated with genomic regions that can be used 198 that contains scores associated with genomic regions that can be used
199 afterwards to plot a heatmap or a profile. 199 afterwards to plot a heatmap or a profile.
200 200
201 Genomic regions can really be anything - genes, parts of genes, ChIP-seq 201 Genomic regions can really be anything - genes, parts of genes, ChIP-seq
202 peaks, favorite genome regions... as long as you provide a proper file 202 peaks, favorite genome regions... as long as you provide a proper file
203 in BED or INTERVAL format. This tool can also be used to filter and sort 203 in BED or INTERVAL format. If you would like to compare different groups of regions
204 regions according to their score. 204 (i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.
205
206 computeMatrix can also be used to filter and sort
207 regions according to their score by making use of its advanced output options.
205 208
206 209
207 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png 210 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
208 :alt: Relationship between computeMatrix, heatmapper and profiler 211 :alt: Relationship between computeMatrix, heatmapper and profiler
209 212
210 213
211 You can find more details in the `computeMatrix wiki`_. 214 You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
212
213 .. _computeMatrix wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
214 215
215 216
216 ----- 217 -----
217 218
218 @REFERENCES@ 219 @REFERENCES@