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This is an efficient Python/Cython implementation of the semiparametric XL-mHG test for enrichment in ranked lists. The XL-mHG test is an extension of the nonparametric mHG test, which was developed by Dr. Zohar Yakhini and colleagues.
Installation
$ pip install xlmhgGetting started
The xlmhg package provides two functions (one simple and more more advanced) for performing XL-mHG tests. These functions are documented in the User Manual. Here’s a quick example using the “simple” test function:
import xlmhg
stat, cutoff, pval = xlmhg.xlmhg_test(v, X, L)Where: v is the ranked list of 0’s and 1’s, represented by a NumPy array of integers, X and L are the XL-mHG parameters, and the return values have the following meanings:
stat: The XL-mHG test statistic
cutoff: The cutoff at which XL-mHG test statistic was attained
pval: The XL-mHG p-value
Documentation
Please refer to the XL-mHG User Manual (hosted on ReadTheDocs).
Citing XL-mHG
If you use the XL-mHG test in your research, please cite Eden et al. (PLoS Comput Biol, 2007) and Wagner (PLoS One, 2015).
Copyright and License
Copyright (c) 2015-2019 Florian Wagner
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Metadata
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Release files for xlmhg 2.5.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| xlmhg-2.5.4.tar.gz | 146.1 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| xlmhg-2.5.4-cp38-cp38-win_amd64.whl | CPython 3.8 | CPython 3.8 | Windows x86-64 | Details |
| xlmhg-2.5.4-cp38-cp38-manylinux1_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.5+ x86-64 | Details |
| xlmhg-2.5.4-cp38-cp38-manylinux1_i686.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.5+ x86-32 | Details |
| xlmhg-2.5.4-cp38-cp38-macosx_10_9_x86_64.whl | CPython 3.8 | CPython 3.8 | macOS 10.9+ x86-64 | Details |
| xlmhg-2.5.4-cp37-cp37m-win_amd64.whl | CPython 3.7 | CPython 3.7 pymalloc | Windows x86-64 | Details |
| xlmhg-2.5.4-cp37-cp37m-win32.whl | CPython 3.7 | CPython 3.7 pymalloc | Windows x86-32 | Details |
| xlmhg-2.5.4-cp37-cp37m-manylinux1_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| xlmhg-2.5.4-cp37-cp37m-manylinux1_i686.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.5+ x86-32 | Details |
| xlmhg-2.5.4-cp37-cp37m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | macOS 10.9+ x86-64, macOS 10.6+ x86-64, macOS 10.10+ x86-64 | Details |
| xlmhg-2.5.4-cp36-cp36m-win_amd64.whl | CPython 3.6 | CPython 3.6 pymalloc | Windows x86-64 | Details |
| xlmhg-2.5.4-cp36-cp36m-win32.whl | CPython 3.6 | CPython 3.6 pymalloc | Windows x86-32 | Details |
| xlmhg-2.5.4-cp36-cp36m-manylinux1_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| xlmhg-2.5.4-cp36-cp36m-manylinux1_i686.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.5+ x86-32 | Details |
| xlmhg-2.5.4-cp36-cp36m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | macOS 10.9+ x86-64, macOS 10.6+ x86-64, macOS 10.10+ x86-64 | Details |
| xlmhg-2.5.4-cp35-cp35m-manylinux1_x86_64.whl | CPython 3.5 | CPython 3.5 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| xlmhg-2.5.4-cp35-cp35m-manylinux1_i686.whl | CPython 3.5 | CPython 3.5 pymalloc | Linux glibc 2.5+ x86-32 | Details |
| xlmhg-2.5.4-cp35-cp35m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl | CPython 3.5 | CPython 3.5 pymalloc | macOS 10.9+ x86-64, macOS 10.10+ x86-64, macOS 10.6+ x86-64 | Details |
Total release size: 3.4 MB
Release files / xlmhg-2.5.4.tar.gz
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Release files / xlmhg-2.5.4-cp38-cp38-manylinux1_x86_64.whl
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twine/1.15.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/44.0.0 requests-toolbelt/0.9.1 tqdm/4.41.1 CPython/3.5.6
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