comparison hicPCA.xml @ 5:dbf4afa03b00 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7

4:38a612a120a8

Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``hicPlotTADs`` or ``hicPlotMatrix``.

For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.

.. image:: $PATH_TO_IMAGES/hicPCA.png
   :width: 60 %

_________________

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

5:dbf4afa03b00

Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``hicPlotTADs`` or ``hicPlotMatrix``.

For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.

.. image:: $PATH_TO_IMAGES/hicPCA.png
   :scale: 35 %

_________________

| For more information about HiCExplorer please consider our documentation on readthedocs.io_