fisher

Fishers Exact Test for Python (Cython)

https://github.com/brentp/fishers_exact_test

Science Score: 36.0%

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Committers with academic emails
3 of 13 committers (23.1%) from academic institutions
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Scientific vocabulary similarity
Low similarity (7.2%) to scientific vocabulary

Keywords from Contributors

bioinformatics genome

Last synced: 10 months ago · JSON representation

Repository

Fishers Exact Test for Python (Cython)

Basic Info

Host: GitHub
Owner: brentp
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage:
Size: 431 KB

Statistics

Stars: 65
Watchers: 4
Forks: 23
Open Issues: 23
Releases: 0

Created over 16 years ago · Last pushed over 1 year ago

Metadata Files

Readme License

README.md

Fisher\'s Exact Test

Simple, fast implementation of Fisher\'s exact test. For example, for the following table:

| | Having the property | Not having the property | | ------------ | ------------------- | ----------------------- | | Selected | 12 | 5 | | Not selected | 29 | 2 |

Perhaps we are interested in whether there is any difference of property in selected vs. non-selected groups, then we can do the Fisher\'s exact test.

Installation

Within this folder :

git clone git://github.com/brentp/fishers_exact_test.git
pip install .

From PyPI :

pip install fisher

Or install the development version :

pip install git+git://github.com/brentp/fishers_exact_test.git

Usage

fisher.pvalue() accepts 4 values corresponding to the 2-by-2 contingency table, returns an object with attributes for lefttail, righttail, and two_tail p-values :

>>> from fisher import pvalue
>>> mat = [[12, 5], [29, 2]]
>>> p = pvalue(12, 5, 29, 2)
>>> p.left_tail, p.right_tail, p.two_tail  # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS
(0.04455473783507..., 0.994525206021..., 0.0802685520741...)

Benchmark

A simple benchmark that calls the Fisher\'s exact test 1000 times (in scripts/rfisher.py):

calling python fisher...
iterations/sec: 3000.62526381
calling rpy fisher...
iterations/sec: 289.225902364
calling R directly...
iterations/sec: 244.36542276

So the cython fisher is up to 10 times faster than rpy or R version.

Owner

Name: Brent Pedersen
Login: brentp
Kind: user
Location: Oregon, USA

Twitter: brent_p
Repositories: 220
Profile: https://github.com/brentp

Doing genomics

GitHub Events

Total

Issues event: 1
Watch event: 2
Delete event: 1
Issue comment event: 10
Push event: 17
Pull request review comment event: 8
Pull request review event: 2
Pull request event: 3
Fork event: 2

Last Year

Issues event: 1
Watch event: 2
Delete event: 1
Issue comment event: 10
Push event: 17
Pull request review comment event: 8
Pull request review event: 2
Pull request event: 3
Fork event: 2

Committers

Last synced: about 1 year ago

All Time

Total Commits: 42
Total Committers: 13
Avg Commits per committer: 3.231
Development Distribution Score (DDS): 0.548

Past Year

Commits: 2
Committers: 2
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Brent Pedersen	b**e@g**m	19
Martin Larralde	m**e@e**e	6
Haibao Tang	t**o@g**m	6
daler	d**r@n**v	2
shouldsee	s**m@g**m	1
marco.mariotti	m**m@g**m	1
Sergei Lebedev	s**y@g**m	1
Mikael Brandström Durling	m**l@d**e	1
Joshua Adelman	s****s	1
Fabio Ticconi	f**i@g**m	1
Dan Bolser	d**r@g**m	1
Christoph Gohlke	c**e@u**u	1
mikaelb	m**b@m**e	1

Committer Domains (Top 20 + Academic)

my-mgrid.mykopat.slu.se: 1 uci.edu: 1 durling.se: 1 niddk.nih.gov: 1 embl.de: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 33
Total pull requests: 19
Average time to close issues: 11 months
Average time to close pull requests: about 1 month
Total issue authors: 30
Total pull request authors: 14
Average comments per issue: 2.42
Average comments per pull request: 2.42
Merged pull requests: 17
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 2
Pull requests: 3
Average time to close issues: N/A
Average time to close pull requests: 2 months
Issue authors: 2
Pull request authors: 3
Average comments per issue: 7.5
Average comments per pull request: 0.67
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

timase2021 (2)
naman-nference (2)
johanneskoester (2)
gserrano92 (1)
edunham (1)
AndreaRMICL (1)
PauBadiaM (1)
yunesj (1)
i000 (1)
paidi (1)
tristanbrown (1)
endrebak (1)
davidnarganes (1)
deto (1)
marco-mariotti (1)

Pull Request Authors

althonos (6)
dbolser (2)
marco-mariotti (2)
dependabot[bot] (2)
superbobry (1)
synapticarbors (1)
bli25 (1)
daler (1)
fabio-t (1)
cgohlke (1)
brentp (1)
shouldsee (1)
mikdur (1)
tanghaibao (1)

Top Labels

Issue Labels

duplicate (1)

Pull Request Labels

dependencies (2)

Packages

Total packages: 3
Total downloads:
- pypi 1,173 last-month
Total docker downloads: 18,154

Total dependent packages: 11
(may contain duplicates)
Total dependent repositories: 42
(may contain duplicates)
Total versions: 14
Total maintainers: 2

pypi.org: fisher

Fast Fisher's Exact Test

Homepage: http://github.com/brentp/fishers_exact_test
Documentation: https://fisher.readthedocs.io/
License: BSD
Latest release: 0.1.14
published almost 3 years ago

Versions: 10
Dependent Packages: 9
Dependent Repositories: 42
Downloads: 1,173 Last month
Docker Downloads: 18,154

Rankings

Dependent packages count: 1.4%

Dependent repos count: 2.3%

Docker downloads count: 3.1%

Average: 4.8%

Downloads: 5.2%

Forks count: 8.2%

Stargazers count: 8.7%

Maintainers (1)

brentp

Last synced: 10 months ago

spack.io: py-fisher

Fisher's Exact Test. Simple, fast implementation of Fisher's exact test.

Homepage: https://github.com/brentp/fishers_exact_test
License: []
Latest release: 0.1.10
published over 3 years ago

Versions: 2
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Average: 17.2%

Stargazers count: 20.3%

Forks count: 20.5%

Dependent packages count: 28.1%

Maintainers (1)

adamjstewart

Last synced: 10 months ago

conda-forge.org: fisher

Homepage: http://github.com/brentp/fishers_exact_test
License: BSD-3-Clause
Latest release: 0.1.9
published almost 7 years ago

Versions: 2
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent packages count: 28.8%

Average: 33.0%

Forks count: 33.9%

Dependent repos count: 34.0%

Stargazers count: 35.3%

Last synced: 11 months ago

Dependencies

requirements.txt pypi

numpy *
pytest *

setup.py pypi

numpy *