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PotentialIntegration
Eaton edited this page Jan 15, 2019
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- RNA-Seq analysis
- Network visualization
- Python graph-tool
- RNA-Seq isoform visualization (requires Matplotlib and PyML)
- 2D and 3D Graphics in Python
- Advanced table viewer
- Interactive heatmap, network and other in Orange
- Methylation-sequencing visualization
- Interactive visualization
- Biclustering
- Sircah
- Sub-pathway based python GSEA DiffPath
- HTSeq
- Exon expression extraction
- PCA and clustering
- RNA-Seq QC and visualization
- RNA-Seq QC and visualization
- Evaluate ICA for LineageProfiler
- Genomic evaluation of qPCR primers
- Databases for probe-level splicing analyses
- GEO data import
- Sweave for python
- SplicingCompass in R
- Pycogent for probabilist genomics
Note: Win32 and Win64 unofficial installers can be found here
easy_install python-graph-core
-
easy_install python-graph-dot
(possible dependency) - install graphviz (dependency for dot and graphviz)
- install MacPorts (easy install for mac apps - from dmg)
- sudo install graphviz
- Ran example python-graph file and received a warning about trying to import the module gv. The module gv appears to be local to python graph and is called when graphviz is found in the indicated path (path is manually specified in the test code). No graphviz folder containing a folder named python found. No solution on the Wiki for mac.
- Tried to install pygraphviz (not sure if this is related) using
easy_install
, does not appear to be related. - Stopped here... failed.
Saw on Stack Overflow that pyGraphViz can run virtually the same example and work without using the above python-graph... this worked! Use this instead (only dependency is graphviz and possibly dot - not sure). Need to test on PC and Linux.
- Depends on numpy (already installed)
-
easy_install matplotlib
... encountered several errors, but installed. As an alternative can install from here (installs numpy). - Tried this - worked great!
- Tried the animation examples on the website and encountered a common error:
- File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib-1.1.0-py2.7-macosx-10.6-intel.egg/matplotlib/animation.py", line 248, in _blit_clear a.figure.canvas.restore_region(bg_cache[a])
- AttributeError: 'FigureCanvasMac' object has no attribute 'restore_region'
- No function restore_region in the class FigureCanvasMac in the module “backend_macosx.py” (only one that contains FigureCanvasMac).
- After contacting the MatPlotLib community, discovered that setting
blit=False
will fix this problem.