ipyrad

Interactive assembly and analysis of RAD-seq data sets

https://github.com/dereneaton/ipyrad

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
6 of 27 committers (22.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary

Keywords

assembly genomics phylogeny rad-seq

Keywords from Contributors

bioinformatics

Last synced: 6 months ago · JSON representation

Repository

Interactive assembly and analysis of RAD-seq data sets

Basic Info

Host: GitHub
Owner: dereneaton
License: gpl-3.0
Language: Jupyter Notebook
Default Branch: master
Homepage: http://ipyrad.readthedocs.io
Size: 98.9 MB

Statistics

Stars: 77
Watchers: 5
Forks: 40
Open Issues: 66
Releases: 20

Topics

assembly genomics phylogeny rad-seq

Created over 10 years ago · Last pushed 8 months ago

Metadata Files

Readme License Support

README.rst

*ipyrad*: interactive assembly and analysis of RAD-seq data sets
--------------------------------------------------------------

Welcome to ipyrad, an interactive toolkit for assembly and analysis of 
restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) 
for population genetic and phylogenetic studies.

Documentation
---------
Full documentation is available here (``_),
where you will find installation instructions, example tutorials, and a full user guide.


Quick Install
------------
ipyrad is available through the Python package installer `conda` with all dependencies included.
If you have `conda` installed you can simply run:

    conda install ipyrad -c conda-forge -c bioconda


If you do not have `conda` installed then you will enjoy our 
`complete installation instructions `_.

Run ipyrad in Binder
--------------------
.. image:: https://mybinder.org/badge_logo.svg
    :alt: Launch ipyrad in a binder instance
    :target: https://mybinder.org/v2/gh/dereneaton/ipyrad/master

Getting Help
------------
Join the ipyrad gitter channel and ask a question, request a feature, or flame the developers:

.. image:: https://badges.gitter.im/Join%20Chat.svg
   :alt: Join the chat at https://gitter.im/dereneaton/ipyrad
   :target: https://gitter.im/dereneaton/ipyrad?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge


License
-------
GPLv3

Cite the Manuscript
-------------------
Eaton DAR & Overcast I. "ipyrad: Interactive assembly and analysis of RADseq datasets." Bioinformatics (2020).

Contributors
------------
+ `Deren Eaton `_  
+ `Isaac Overcast `_

Owner

Name: Deren Eaton
Login: dereneaton
Kind: user
Location: NYC
Company: Columbia University

Website: https://www.eaton-lab.org
Repositories: 24
Profile: https://github.com/dereneaton

Botany | Genomics | Admixture | Phylogeny

GitHub Events

Total

Create event: 3
Release event: 1
Issues event: 33
Watch event: 4
Issue comment event: 59
Push event: 25
Fork event: 1

Last Year

Create event: 3
Release event: 1
Issues event: 33
Watch event: 4
Issue comment event: 59
Push event: 25
Fork event: 1

Committers

Last synced: 9 months ago

All Time

Total Commits: 3,988
Total Committers: 27
Avg Commits per committer: 147.704
Development Distribution Score (DDS): 0.431

Past Year

Commits: 56
Committers: 2
Avg Commits per committer: 28.0
Development Distribution Score (DDS): 0.375

Top Committers

Name	Email	Commits
dereneaton	d**n@y**u	2,268
Isaac Overcast	i**t@g**m	1,077
eaton-lab	d**6@c**u	499
isaacovercast	l**r@T**l	52
Francisco Pina Martins	f**s@g**m	16
Isaac	i**t@n**r	16
isaac	i**c@Y**l	15
Isaac	i**t@n**r	9
Fishlab	f**b@F**l	7
Carlos Alonso Maya Lastra	c****l	4
Isaac	i**t@n**r	4
Isaac	i**t@Y**l	4
Tankred Ott	T**t@h**e	2
Oliver Stueker	o****r	2
deren eaton	d**6@t**r	1
deren eaton	d**6@t**r	1
deren eaton	d**6@t**r	1
deren eaton	d**6@s**r	1
Maia Hernandez	m**z@d**u	1
Maia Hernandez	m**z@d**u	1
Isaac Overcast	i**t@p**u	1
Isaac	i**t@n**r	1
Anonymous	a**s@o**m	1
Deren Eaton	d**n@s**u	1
Edgardo M. Ortiz	e**v@g**m	1
Mike Renfro	m**b@r**o	1
The Gitter Badger	b**r@g**m	1

Committer Domains (Top 20 + Academic)

gitter.im: 1 renf.ro: 1 sacra.columbia.edu: 1 overleaf.com: 1 node002.cm.cluster: 1 penzias.csi.cuny.edu: 1 dyn-209-2-208-172.dyn.columbia.edu: 1 dyn-209-2-208-78.dyn.columbia.edu: 1 shake.cm.cluster: 1 t103.cm.cluster: 1 t107.cm.cluster: 1 t110.cm.cluster: 1 hotmail.de: 1 node003.cm.cluster: 1 fishlabs-mini.wireless.yale.internal: 1 node004.cm.cluster: 1 node001.cm.cluster: 1 columbia.edu: 1 yale.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 187
Total pull requests: 7
Average time to close issues: 5 months
Average time to close pull requests: 1 day
Total issue authors: 95
Total pull request authors: 4
Average comments per issue: 3.86
Average comments per pull request: 1.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 29
Pull requests: 0
Average time to close issues: 3 days
Average time to close pull requests: N/A
Issue authors: 19
Pull request authors: 0
Average comments per issue: 1.31
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

isaacovercast (46)
alexkrohn (10)
zilaijuand (4)
carlahurt (4)
jljy47 (4)
tsm-tsm (4)
jesus-mavarez (3)
amesclir (3)
c-mccarron (3)
AliBasuony2022 (3)
urigarciaunam (3)
mydjc (3)
edgagnon (2)
ospfsg (2)
aroavaron (2)

Pull Request Authors

camayal (2)
TankredO (2)
mikerenfro (2)
stephamor (1)

Top Labels

Issue Labels

enhancement (3)

Pull Request Labels

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 2
(may contain duplicates)
Total versions: 11
Total maintainers: 1

pypi.org: ipyrad

Interactive assembly and analysis of RADseq data sets

Homepage: https://github.com/dereneaton/ipyrad
Documentation: https://ipyrad.readthedocs.io/
License: GPL
Latest release: 0.1.32
published about 10 years ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 0
Docker Downloads: 0

Rankings

Dependent packages count: 5.9%

Forks count: 6.0%

Dependent repos count: 7.9%

Stargazers count: 8.2%

Average: 13.6%

Downloads: 40.1%

Last synced: about 1 year ago

spack.io: py-ipyrad

An interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

Homepage: https://github.com/dereneaton/ipyrad
License: []
Latest release: 0.9.102
published about 1 year ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 16.7%

Stargazers count: 20.7%

Average: 23.7%

Dependent packages count: 57.2%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

Dependencies

binder/environment.yml conda

bcftools
bpp
bucky
clumpp
htslib
ipcoal
ipyrad
mrbayes
raxml
scikit-learn
structure
tetrad
toytree
treemix

docs/requirements.txt pypi

ipykernel *
nbsphinx *
sphinx >=1.4
sphinx_rtd_theme *

newdocs/requirements.txt pypi

ipykernel *
jinja2 <3.0.0
nbsphinx *
sphinx >=1.4
sphinx_rtd_theme *

setup.py pypi

cutadapt *
future *
h5py *
ipyparallel *
numba *
numpy *
pandas *
pysam *
requests *
scipy *