Anaconda(or Miniconda) -> Python 3.x
If you are running windows we suggest that you install Miniconda3 in %PROGRAMFILES%\Miniconda3 without adding it to your windows path. This way it should not interfere with other installations of Python.
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Make sure your computer has Miniconda3/Anaconda3 installed. You can download the free software from the links listed above.
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Download and unzip the this zip file
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Open a commandline windows as administrator (press the windows button then type cmd) or teminal (linux users should how to do this, mac users just google it).
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If Python 3.x is already available on your system path and you know what you are doing skip to step 4.
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In the commandline activate Anaconda/Miniconda by typing the following:
"%PROGRAMFILES%\Miniconda3\Scripts\activate.bat"or
"%PROGRAMFILES%\Anaconda3\Scripts\activate.bat" -
Your commandline now be prepended with the word
(base). -
cdto the unzipped directory from step 1 like so:cd %userprofile%\Downloads\omin-master\ -
Then run the command:
pip install . -
This command will install the omin package into:
<Your Python distro>\lib\sitepackages. Now omin can be run from the command-line or imported into jupyter notebook.
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Initialize the software
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Drag and drop the peptide isoforms file and proteins file from the Proteome Discoverer analysis into a folder with the name Raw_Data at the same level as the notebook
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Create the process object
procusing the command in cell 3. Can also see meta-data on the from the peptides and proteins by using the commands in cells 4 and 5
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Check that the study factors were isolated correctly by using the command in cell 6
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Check to see if the peptide groups were normalized by using the commands in cell 7
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Then create a mask for the enriched modification you would like to examine using the command in cell 8. Also we can see the result object initialized in cell 10
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In cell 11 we can see the creation of the interactive of the volcano plot for the peptide relative abundance
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In cell 12 the we are comparing the NR fraction to the fraction without NR in the relative occupancy of the acetyl-peptides and adding that to the result object. That result object is exported to a csv in cell 14. In cell 13 we see the creation of the volcano plot that was made
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Comparisons in protein expression is made in a simillar way in cell 24
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The interactive volcano plot for the protein expression is made in cell 25 and the protein expression data is exported using the command in cell 26
State diagrams generated with FreeMind 1.0.1
Want to help? Check the to do list kill the bugs, make a PR, and bask in the glory✼.
✼: Amount of glory with vary based on bug squashed.
Copyright 2018 James Draper, Paul Grimsrud, Deborah Muoio, Colette Blach, Blair Chesnut, and Elizabeth Hauser.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files, Omics Modeling Integrating Normalization (OMIN), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM. OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.