geoparse
Python library to access Gene Expression Omnibus Database (GEO)
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 21 committers (9.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Keywords
bioinformatics
geo-database
high-throughput-sequencing
htseq
microarray
rna-seq
rna-sequencing
Keywords from Contributors
genome
bgzf
dna
fasta
indexing
protein
samtools
Last synced: 6 months ago
·
JSON representation
Repository
Python library to access Gene Expression Omnibus Database (GEO)
Basic Info
- Host: GitHub
- Owner: guma44
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: master
- Size: 13.3 MB
Statistics
- Stars: 152
- Watchers: 7
- Forks: 50
- Open Issues: 23
- Releases: 0
Topics
bioinformatics
geo-database
high-throughput-sequencing
htseq
microarray
rna-seq
rna-sequencing
Created over 10 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
Changelog
Contributing
License
Authors
README.rst
===============================
GEOparse
===============================
.. image:: https://img.shields.io/pypi/v/GEOparse.svg
:target: https://pypi.python.org/pypi/GEOparse
.. image:: https://img.shields.io/travis/guma44/GEOparse.svg
:target: https://travis-ci.org/guma44/GEOparse
Python library to access Gene Expression Omnibus Database (GEO).
GEOparse is python package that can be used to query and retrieve data from Gene Expression Omnibus database (GEO).
The inspiration and the base for it is great R library GEOquery.
* Free software: BSD license
* Documentation: https://GEOparse.readthedocs.org.
Features
--------
* Download GEO series, datasets etc. as SOFT files
* Download supplementary files for GEO series to use them locally
* Load GEO SOFT as easy to use and manipulate objects
* Prepare your data for GEO upload
Installation
------------
At the command line::
$ pip install GEOparse
TODO
----
There is still work to do so any contribution is welcome. Any bug/error that you report
will improve the library.
The main issues are:
* add checking for compatibility with SOFT files
* expand GEOTypes objects with useful functions for differential expression analysis
* share your idea
* add more tests - that's always good idea :)
Owner
- Name: Rafal Gumienny
- Login: guma44
- Kind: user
- Location: Basel, CH
- Company: Novartis
- Website: guma44.github.io
- Repositories: 3
- Profile: https://github.com/guma44
Scientific Software Engineer at Novartis Institutes for BioMedical Research (NIBR)
GitHub Events
Total
- Watch event: 15
- Fork event: 2
Last Year
- Watch event: 15
- Fork event: 2
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Rafal Gumienny | g****4@g****m | 138 |
| Rafal Gumienny | r****y@u****h | 30 |
| simonvh | s****n@g****m | 14 |
| Haries Ramdhani | h****e@g****m | 5 |
| tatsu | t****1@g****m | 5 |
| Tycho Bismeijer | t****r@n****l | 2 |
| Rafal Gumienny | g****1@c****t | 2 |
| Kurt Wheeler | k****1@g****m | 2 |
| Aleksandra Galitsyna | a****a@m****h | 2 |
| Kwat | K****E | 1 |
| Michael von Papen | 2****n | 1 |
| William C Grisaitis | w****s@g****m | 1 |
| Zhongjie He | e****6 | 1 |
| Alejandro Barrera | a****a@d****u | 1 |
| Aleksandra Galitsyna | a****a@g****m | 1 |
| BioIndoData | r****s@g****m | 1 |
| Maarten-vd-Sande | m****e@h****m | 1 |
| Michael Lampe | M****e@g****m | 1 |
| Rafal Gumienny | r****y@n****m | 1 |
| Rafal Gumienny | r****y@p****m | 1 |
| Rich Jones | m****u@g****m | 1 |
Committer Domains (Top 20 + Academic)
novartis.com: 1
duke.edu: 1
mgmt.cobrain.stech: 1
c02xw1majgh6.eu.novartis.net: 1
nki.nl: 1
unibas.ch: 1
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 59
- Total pull requests: 26
- Average time to close issues: about 2 months
- Average time to close pull requests: 3 months
- Total issue authors: 37
- Total pull request authors: 18
- Average comments per issue: 2.22
- Average comments per pull request: 1.42
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- antonkulaga (10)
- Miserlou (7)
- halioui (3)
- tyasird (3)
- KwatMDPhD (2)
- abysslover (2)
- CholoTook (2)
- n1mus (1)
- liugaocn (1)
- jonasfreimuth (1)
- RemyLau (1)
- dtenenba (1)
- ruxi (1)
- Mengflz (1)
- vttrifonov (1)
Pull Request Authors
- simonvh (5)
- KwatMDPhD (3)
- guma44 (2)
- olp-cs (2)
- ttyskg (2)
- kurtwheeler (2)
- alexbarrera (2)
- agalitsyna (1)
- Miserlou (1)
- eric6356 (1)
- MichaelLampe (1)
- hariesramdhani (1)
- miguelroboso (1)
- tychobismeijer (1)
- BioInfoData (1)
Top Labels
Issue Labels
bug (13)
enhancement (13)
possible enhancement (1)
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 25,424 last-month
- Total docker downloads: 6,652
-
Total dependent packages: 3
(may contain duplicates) -
Total dependent repositories: 6
(may contain duplicates) - Total versions: 24
- Total maintainers: 1
pypi.org: geoparse
Python library to access Gene Expression Omnibus Database (GEO)
- Homepage: https://github.com/guma44/GEOparse
- Documentation: https://geoparse.readthedocs.io/
- License: BSD
-
Latest release: 2.0.4
published almost 2 years ago
Rankings
Docker downloads count: 1.6%
Downloads: 3.0%
Average: 4.7%
Dependent packages count: 4.7%
Forks count: 5.8%
Stargazers count: 6.4%
Dependent repos count: 6.7%
Maintainers (1)
Last synced:
6 months ago
conda-forge.org: geoparse
- Homepage: https://github.com/guma44/GEOparse
- License: BSD-3-Clause
-
Latest release: 2.0.3
published about 4 years ago
Rankings
Dependent packages count: 19.6%
Dependent repos count: 24.2%
Average: 25.2%
Forks count: 25.4%
Stargazers count: 31.6%
Last synced:
6 months ago
Dependencies
requirements.txt
pypi
- black *
- flake8 *
- isort *
- numpy >=1.7
- pandas >=0.21
- pre-commit *
- pytest *
- pytest-cov *
- pytz >=2013
- requests >=2.21.0
- sphinxcontrib-napoleon >=0.6.1
- tqdm >=4.31.1
setup.py
pypi