oxbow

(★ 169)

Oxbow makes genomic data ready for high-performance analytics.

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- - ci.yml
  - pull_request_template.md
  - release-python.yml
  - release-rust.yml
- CODE_OF_CONDUCT.md
- dependabot.yaml
- - favicon.ico
  - icon_book.svg
  - icon_branch.svg
  - icon_code.svg
  - logo.svg
  - oxbow-arrow-diagram.svg
  - oxbow-logo-wide-black.svg
  - oxbow-logo-wide-white.svg
  - oxbow-logo.svg
  - style.css
  - switcher.json
- - version.html
- - index.md
  - python.rst
  - r.md
- - development.md
  - documentation.md
  - index.md
- - data
  - index.md
  - installation.md
  - quickstart.md
  - why.md
- - coordinate-systems.md
  - index.md
  - matrix.md
- conf.py
- index.rst
- autosql-sample.bb
- ENCFF758CQW.100.bed.gz
- example.gff
- example.gtf
- list.txt
- malformed.bam
- malformed.bb
- malformed.bcf
- malformed.bed
- malformed.bw
- malformed.cram
- malformed.fasta
- malformed.fastq
- malformed.gff
- malformed.gtf
- malformed.sam
- README.md
- sample-ref.cram
- sample-ref.cram.crai
- sample-ref.fa
- sample-ref.fa.fai
- sample-ref.sam
- sample.bam
- sample.bam.bai
- sample.bb
- sample.bcf
- sample.bcf.csi
- sample.bed
- sample.bed.gz
- sample.bed.gz.tbi
- sample.bw
- sample.cram
- sample.cram.crai
- sample.fasta
- sample.fasta.fai
- sample.fasta.gz
- sample.fasta.gz.gzi
- sample.fastq
- sample.fastq.bgz
- sample.fastq.bgz.gzi
- sample.fastq.gz
- sample.gff
- sample.gtf
- sample.sam
- sample.sam.gz
- sample.sam.gz.tbi
- sample.sorted.gff
- sample.sorted.gff.gz
- sample.sorted.gff.gz.tbi
- sample.sorted.gtf
- sample.sorted.gtf.gz
- sample.sorted.gtf.gz.tbi
- sample.ubam
- sample.ubcf
- sample.vcf
- sample.vcf.gz
- sample.vcf.gz.csi
- sample.vcf.gz.tbi
- - alignment.rs
  - batch.rs
  - bbi.rs
  - bed.rs
  - coords.rs
  - error.rs
  - gxf.rs
  - lib.rs
  - sequence.rs
  - util.rs
  - variant.rs
- Cargo.lock
- Cargo.toml
- LICENSE-APACHE
- LICENSE-MIT
- README.md
- - bench.ipynb
- - __init__.py
  - _filetypes.py
  - _pyarrow.py
  - arrow.py
  - core.py
  - py.typed
- - alignment.rs
  - bbi.rs
  - bed.rs
  - error.rs
  - filelike.rs
  - gxf.rs
  - lib.rs
  - sequence.rs
  - util.rs
  - variant.rs
- - conftest.py
  - data
  - test_alignment.py
  - test_base.py
  - test_bbi.py
  - test_bed.py
  - test_coords.py
  - test_gxf.py
  - test_pyarrow.py
  - test_scanners.py
  - test_sequence.py
  - test_variant.py
  - utils.py
  - wiretap.py
- Cargo.toml
- pyproject.toml
- README.md
- uv.lock
- - api.R
  - extendr-wrappers.R
- - .gitignore
  - entrypoint.c
  - Makevars
  - Makevars.ucrt
  - Makevars.win
  - oxbow-win.def
- DESCRIPTION
- NAMESPACE
- README.md
.gitattributes
.gitignore
.readthedocs.yaml
Cargo.lock
Cargo.toml
LICENSE-APACHE
LICENSE-MIT
README.md
rust-toolchain.toml

# Installation Guide

1. Get the code

git clone https://github.com/abdenlab/oxbow

Downloads the entire project code from GitHub to your computer.

cd oxbow

Moves into the project folder you just downloaded.

2. Python

Easy Recommended

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

pip install .

Installs the package published on PyPI directly — no need to clone the source.

jupyter notebook

Launches Jupyter in your browser so you can open and run the notebook (.ipynb) files.

✅ If it runs without errors and prints output in the terminal, it worked.

3. Rust

Medium

Prerequisites

Git Needed to download the project code from GitHub.
Rust (rustup) Installing via rustup also installs cargo.

cargo build --release

Compiles the Rust project.

cargo run

Builds and then immediately runs the program.

✅ If cargo build finishes without errors, it worked. The executable is created under target/.

oxbow

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# Installation Guide

2. Python

3. Rust

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oxbow

File Explorer

# Installation Guide

2. Python

3. Rust

Today's picks

Was this content helpful?

Recent Feedback

Download README