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XL-mHG: A Semiparametric Test for Enrichment

Project Description

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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 xlmhg

Getting 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).

Release History

This version
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2.4.9

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2.4.8

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2.4.7

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2.4.6

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2.4.5

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2.4.4

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2.4.3

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2.4.2

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2.4.1

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2.4.0

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2.3.1

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2.3.0

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2.2.12

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2.2.11

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2.2.10

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2.2.9

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2.2.8

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2.2.7

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2.2.6

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2.2.5

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2.2.4

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2.2.3

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2.2.1

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2.2.0

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2.1.1

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2.1.0

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2.0.7

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2.0.6

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2.0.5

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2.0.5rc1

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2.0.4

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2.0.3

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2.0.1

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1.1rc3

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1.1rc2

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1.1rc1

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xlmhg-2.4.9-cp27-cp27m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl
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xlmhg-2.4.9-cp27-cp27mu-manylinux1_i686.whl
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xlmhg-2.4.9-cp34-cp34m-manylinux1_i686.whl
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xlmhg-2.4.9-cp35-cp35m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl
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xlmhg-2.4.9-cp35-cp35m-win_amd64.whl
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xlmhg-2.4.9-cp36-cp36m-macosx_10_6_x86_64.macosx_10_9_x86_64.macosx_10_10_x86_64.whl
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xlmhg-2.4.9-cp36-cp36m-manylinux1_x86_64.whl
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