pycallingcards
Python package designed for single-cell calling cards data
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: sciencedirect.com -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.2%) to scientific vocabulary
Repository
Python package designed for single-cell calling cards data
Basic Info
- Host: GitHub
- Owner: The-Mitra-Lab
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Size: 102 MB
Statistics
- Stars: 16
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Pycallingcards
Pycallingcards is a package for calling cards data analysis developed and maintained by Mitra Lab at Washington University in St. Louis.
Calling cards is a sequencing technology to assay TF binding which could be done in vitro and in vivo at both bulk and single-cell level. To know more about calling cards technology, please check Moudgil et al and Wang et al.
Pycallingcards is composed of five different part: datasets, reading (rd), preprocessing (pp), tools (tl) and plotting (pl). For single-cell calling cards anaysis, Pycallingcards interacts with Scanpy and the main structure of Pycallingcards also follows the Scanpy.
- Datasets contains four main published datasets for callingcards data.
- Reading (rd) includes several functions to read and save qbed and peak data.
- Preprocessing (pp) helps to preprocess data from qbed data to call peaks, make annotation, make Anndata object and filter peaks.
- Tools (tl) calls motif of the peaks, completes differential peaks and pair differential peaks with gene expression,
- Plotting (pl) proveides an allround plottting system. It could plot genome areas, link with WashU Epigenome Browser, show signal comparison with Chip-seq(BigWig file), display differential peaks, demonstrate potenial binding-gene expression relationships.
Documentation.
Please check here for detailed documentation.
Installation
Install via GitHub (Recommended)
shell
pip install "git+https://github.com/The-Mitra-Lab/pycallingcards.git" --upgrade
or
shell
pip install pycallingcards
Docker
Link to dockerhub of pycallingcards here.
Link to tips and codes for using pycallingcards docker here.
Development
Use pre-commit to format code at git commit.
shell
pip install pre-commit
pre-commit install
Cite
bibtex
@article{guo2024pycallingcards,
title={Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting calling cards data},
author={Guo, Juanru and Zhang, Wenjin and Chen, Xuhua and Yen, Allen and Chen, Lucy and Shively, Christian A and Li, Daofeng and Wang, Ting and Dougherty, Joseph D and Mitra, Robi D},
journal={Bioinformatics},
pages={btae070},
year={2024},
publisher={Oxford University Press}
}
Owner
- Name: The-Mitra-Lab
- Login: The-Mitra-Lab
- Kind: organization
- Repositories: 2
- Profile: https://github.com/The-Mitra-Lab
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Guo"
given-names: "Juanru"
- family-names: "Mitra"
given-names: "Robi"
title: "Pycallingcards: Calling Cards Data Analysis in Python"
version: 1.0.0
date-released: 2023-12-19
url: "https://github.com/The-Mitra-Lab/pycallingcards"
GitHub Events
Total
- Watch event: 1
- Member event: 2
- Push event: 3
Last Year
- Watch event: 1
- Member event: 2
- Push event: 3
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 25 days
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.33
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- cmatKhan (2)
- JuanruMaryGuo (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 16 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
pypi.org: pycallingcards
"Calling cards data analysis in Python."
- Homepage: https://github.com/The-Mitra-Lab/pycallingcards
- Documentation: https://pycallingcards.readthedocs.io/
- License: BSD 3-Clause License
-
Latest release: 1.0.0
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- appdirs *
- furo *
- matplotlib *
- numba *
- numpy *
- pandas *
- scanpy *
- scipy *
- sphinx-autoapi *
- tqdm *
- typing *
- appdirs *
- furo *
- liftover *
- matplotlib *
- mudata *
- myst_parser *
- nbsphinx *
- numba *
- numpy *
- pandas *
- pyBigWig *
- pybedtools *
- scanpy *
- scipy *
- seaborn *
- sklearn *
- sphinx *
- sphinx-hoverxref *
- sphinx_autodoc_typehints *
- sphinx_copybutton *
- sphinx_design *
- sphinxcontrib-bibtex *
- sphinxext.opengraph *
- tqdm *
- actions/checkout v4 composite
- actions/setup-python v5 composite
- peaceiris/actions-gh-pages v3 composite