Python reimplementation of mProphet peak scoring
Project description
pyprophet
=========
python reimplementation of mProphet algorithm. For more information, see the following publication:
Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.
*mProphet: automated data processing and statistical validation for large-scale
SRM experiments.* **Nat Methods.** 2011 May;8(5):430-5. [doi:
10.1038/nmeth.1584.](http://dx.doi.org/10.1038/nmeth.1584) Epub 2011 Mar 20.
In short, the algorithm can take targeted proteomics data, learn a linear
separation between true signal and the noise signal and then compute a q-value
(false discovery rate) to achieve experiment-wide cutoffs.
Installation
============
Install *pyprophet* from Python package index:
```
$ pip install numpy
$ pip install pyprophet
```
or:
```
$ easy_install numpy
$ easy_install pyprophet
```
Running pyprophet
=================
*pyoprophet* is not only a Python package, but also a command line tool:
```
$ pyprophet --help
```
or:
```
$ pyprophet --delim=tab tests/test_data.txt
```
Running tests
=============
The *pyprophet* tests are best executed using `py.test`, to run the tests use:
```
$ pip install pytest
$ py.test tests
```
=========
python reimplementation of mProphet algorithm. For more information, see the following publication:
Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.
*mProphet: automated data processing and statistical validation for large-scale
SRM experiments.* **Nat Methods.** 2011 May;8(5):430-5. [doi:
10.1038/nmeth.1584.](http://dx.doi.org/10.1038/nmeth.1584) Epub 2011 Mar 20.
In short, the algorithm can take targeted proteomics data, learn a linear
separation between true signal and the noise signal and then compute a q-value
(false discovery rate) to achieve experiment-wide cutoffs.
Installation
============
Install *pyprophet* from Python package index:
```
$ pip install numpy
$ pip install pyprophet
```
or:
```
$ easy_install numpy
$ easy_install pyprophet
```
Running pyprophet
=================
*pyoprophet* is not only a Python package, but also a command line tool:
```
$ pyprophet --help
```
or:
```
$ pyprophet --delim=tab tests/test_data.txt
```
Running tests
=============
The *pyprophet* tests are best executed using `py.test`, to run the tests use:
```
$ pip install pytest
$ py.test tests
```
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