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Bioframe: Operations on Genomic Interval Dataframes\n\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/bioframe-logo.png\" width=75%\u003e\n\n![CI](https://github.com/open2c/bioframe/actions/workflows/ci.yml/badge.svg)\n[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/open2c/bioframe/main.svg)](https://results.pre-commit.ci/latest/github/open2c/bioframe/main)\n[![Docs status](https://readthedocs.org/projects/bioframe/badge/)](https://bioframe.readthedocs.io/en/latest/)\n[![Paper](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtae088-blue)](https://doi.org/10.1093/bioinformatics/btae088)\n[![Zenodo](https://zenodo.org/badge/69901992.svg)](https://zenodo.org/badge/latestdoi/69901992)\n[![Slack](https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack)](https://bit.ly/open2c-slack)\n[![NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat\u0026colorA=E1523D\u0026colorB=007D8A)](https://www.numfocus.org)\n\nBioframe enables flexible and scalable operations on genomic interval dataframes in Python.\n\nBioframe is built directly on top of [Pandas](https://pandas.pydata.org/). Bioframe provides:\n\n* A variety of genomic interval operations that work directly on dataframes.\n* Operations for special classes of genomic intervals, including chromosome arms and fixed-size bins.\n* Conveniences for diverse tabular genomic data formats and loading genome assembly summary information.\n\nRead the [documentation](https://bioframe.readthedocs.io/en/latest/), including the [guide](https://bioframe.readthedocs.io/en/latest/guide-intervalops.html), as well as the [publication](https://doi.org/10.1093/bioinformatics/btae088) for more information.\n\nBioframe is an Affiliated Project of [NumFOCUS](https://www.numfocus.org).\n\n## Installation\n\nBioframe is available on [PyPI](https://pypi.org/project/bioframe/) and [bioconda](https://bioconda.github.io/recipes/bioframe/README.html):\n\n```sh\npip install bioframe\n```\n\n## Contributing\n\nInterested in contributing to bioframe? That's great! To get started, check out the [contributing guide](https://github.com/open2c/bioframe/blob/main/CONTRIBUTING.md). Discussions about the project roadmap take place on the [Open2C Slack](https://bit.ly/open2c-slack) and regular developer meetings scheduled there. Anyone can join and participate!\n\n\n## Interval operations\n\nKey genomic interval operations in bioframe include:\n- `overlap`: Find pairs of overlapping genomic intervals between two dataframes.\n- `closest`: For every interval in a dataframe, find the closest intervals in a second dataframe.\n- `cluster`: Group overlapping intervals in a dataframe into clusters.\n- `complement`: Find genomic intervals that are not covered by any interval from a dataframe.\n\nBioframe additionally has functions that are frequently used for genomic interval operations and can be expressed as combinations of these core operations and dataframe operations, including: `coverage`, `expand`, `merge`, `select`, and `subtract`.\n\nTo `overlap` two dataframes, call:\n```python\nimport bioframe as bf\n\nbf.overlap(df1, df2)\n```\n\nFor these two input dataframes, with intervals all on the same chromosome:\n\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/df1.png\" width=60%\u003e\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/df2.png\" width=60%\u003e\n\n`overlap` will return the following interval pairs as overlaps:\n\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/overlap_inner_0.png\" width=60%\u003e\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/overlap_inner_1.png\" width=60%\u003e\n\n\nTo `merge` all overlapping intervals in a dataframe, call:\n```python\nimport bioframe as bf\n\nbf.merge(df1)\n```\n\nFor this input dataframe, with intervals all on the same chromosome:\n\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/df1.png\" width=60%\u003e\n\n`merge` will return a new dataframe with these merged intervals:\n\n\u003cimg src=\"https://github.com/open2c/bioframe/raw/main/docs/figs/merge_df1.png\" width=60%\u003e\n\nSee the [guide](https://bioframe.readthedocs.io/en/latest/guide-intervalops.html) for visualizations of other interval operations in bioframe.\n\n## File I/O\n\nBioframe includes utilities for reading genomic file formats into dataframes and vice versa. One handy function is `read_table` which mirrors pandas’s read_csv/read_table but provides a [`schema`](https://github.com/open2c/bioframe/blob/main/bioframe/io/schemas.py) argument to populate column names for common tabular file formats.\n\n```python\njaspar_url = 'http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/hg38/MA0139.1.tsv.gz'\nctcf_motif_calls = bioframe.read_table(jaspar_url, schema='jaspar', skiprows=1)\n```\n\n## Tutorials\nSee this [jupyter notebook](https://github.com/open2c/bioframe/tree/master/docs/tutorials/tutorial_assign_motifs_to_peaks.ipynb) for an example of how to assign TF motifs to ChIP-seq peaks using bioframe.\n\n\n## Citing\n\nIf you use ***bioframe*** in your work, please cite:\n\n```bibtex\n@article{bioframe_2024,\nauthor = {Open2C and Abdennur, Nezar and Fudenberg, Geoffrey and Flyamer, Ilya M and Galitsyna, Aleksandra A and Goloborodko, Anton and Imakaev, Maxim and Venev, Sergey},\ndoi = {10.1093/bioinformatics/btae088},\njournal = {Bioinformatics},\ntitle = {{Bioframe: Operations on Genomic Intervals in Pandas Dataframes}},\nyear = {2024}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopen2c%2Fbioframe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopen2c%2Fbioframe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopen2c%2Fbioframe/lists"}