https://github.com/afrendeiro/toolkit

A toolkit for NGS analysis with Python
https://github.com/afrendeiro/toolkit

Keywords

atac-seq bioinformatics chip-seq looper ngs ngs-analysis project-management pypiper rna-seq

Last synced: 11 months ago
JSON representation

Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

Repository metadata

A toolkit for NGS analysis with Python

Host: GitHub
URL: https://github.com/afrendeiro/toolkit
Owner: afrendeiro
License: gpl-3.0
Created: 2017-05-30T16:59:13.000Z (almost 8 years ago)
Default Branch: master
Last Pushed: 2023-01-18T17:12:08.000Z (over 2 years ago)
Last Synced: 2024-04-25T09:01:31.483Z (about 1 year ago)
Topics: atac-seq, bioinformatics, chip-seq, looper, ngs, ngs-analysis, project-management, pypiper, rna-seq
Language: Python
Homepage: http://ngs-toolkit.readthedocs.io
Size: 1.56 MB
Stars: 13
Watchers: 4
Forks: 4
Open Issues: 13
Releases: 0
Metadata Files:
- Readme: README.md

Owner metadata

Name: André F. Rendeiro
Login: afrendeiro
Email:
Kind: user
Description: Principal Investigator at CeMM - Research Center for Molecular Medicine, Vienna Austria; Leading @rendeirolab; he/him
Website: https://andre-rendeiro.com
Location: Vienna, Austria
Twitter: afrendeiro
Company: CeMM - Research Center for Molecular Medicine
Icon url: https://avatars.githubusercontent.com/u/2065206?v=4
Repositories: 22
Last ynced at: 2023-04-11T18:14:53.380Z
Profile URL: https://github.com/afrendeiro

GitHub Events

Total

Create event: 54
Commit comment event: 1
Release event: 17
Issues event: 90
Watch event: 16
Delete event: 10
Issue comment event: 48
Member event: 1
Push event: 532
Pull request event: 27
Fork event: 8

Last Year

Watch event: 1

Name	Email	Commits
Andre Rendeiro	a**o@g**m	675
fwzhao	f**o@g**m	3
André Rendeiro	a**o@c**t	2

Issue and Pull Request metadata

Last synced: 12 months ago

Total issues: 55
Total pull requests: 14
Average time to close issues: 4 months
Average time to close pull requests: 7 days
Total issue authors: 4
Total pull request authors: 3
Average comments per issue: 0.82
Average comments per pull request: 0.29
Merged pull request: 11
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 0
Past year pull request authors: 0
Past year average comments per issue: 0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/afrendeiro/toolkit

Top Issue Authors

afrendeiro (28)
fwzhao (25)
nsheff (1)
sreichl (1)

Top Pull Request Authors

afrendeiro (9)
fwzhao (4)
codacy-badger (1)

Top Issue Labels

enhancement (16)
bug (12)
tests (3)
api (2)
new feature (2)
wontfix (1)
duplicate (1)

Top Pull Request Labels

Package metadata

Total packages: 1
Total downloads:
- pypi: 137 last-month
Total dependent packages: 0
Total dependent repositories: 1
Total versions: 31
Total maintainers: 1

pypi.org: ngs-toolkit

A toolkit for NGS analysis with Python.

Homepage: https://github.com/afrendeiro/toolkit
Documentation: https://ngs-toolkit.readthedocs.io
Licenses: GPL3
Latest release: 0.25.1 (published over 4 years ago)
Last Synced: 2024-05-26T02:01:46.082Z (12 months ago)
Versions: 31
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 137 Last month
Rankings:
- Dependent packages count: 10.103%
- Forks count: 15.375%
- Stargazers count: 15.64%
- Average: 16.167%
- Downloads: 18.112%
- Dependent repos count: 21.607%
Maintainers (1)
- afrendeiro

Dependencies

requirements/requirements.docs.txt pypi

Sphinx *
sphinx-argparse *
sphinx-issues *
sphinx_rtd_theme *

requirements/requirements.single_cell.txt pypi

fa2 *
fbpca *
leidenalg *
loompy *
louvain >=0.6
phate *
python-igraph *
scanorama *
scanpy *
scvelo *

requirements/requirements.test.txt pypi

codacy-coverage * test
codecov * test
coverage >=4.5.2 test
pytest >=4.4.0 test
pytest-cov * test
pytest-xdist * test
rpy2 >=3.2.0 test

requirements/requirements.txt pypi

attmap >=0.12.11
divvy >=0.5.0
fastcluster *
jinja2 >=2.10.1
joblib >=0.12.5
matplotlib *
natsort >=6.0.0
numpy >=1.15.0
pandas >=0.25.0
parmap >=1.5.1
patsy >=0.4.1
peppy >=0.30.1
pybedtools >=0.7.10
pysam >=0.13
requests >=2.21.0
scikit-learn >=0.19.1
scipy >=1.0.0
seaborn >=0.10.0
setuptools_scm >=3.3.3
statsmodels >=0.8.0
tqdm >=4.19.5

.github/workflows/test.yaml actions

actions/checkout v1 composite
actions/setup-python v1 composite

Dockerfile docker

gitpod/workspace-full-vnc latest build

Score: 9.291182759820284

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Sustainable Technology