Metadata-Version: 2.3
Name: ogtk
Version: 0.1.1
Summary: General tools for genomics and lineage tracing
Project-URL: Home-page, https://github.com/tzeitim/ogtk
Author: Pedro Olivares
Maintainer-email: Pedro Olivares <pedroy.final@gmail.com>
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Rust
Requires-Dist: bgzip
Requires-Dist: colorhash
Requires-Dist: fastcluster
Requires-Dist: fastparquet
Requires-Dist: hdbscan
Requires-Dist: matplotlib
Requires-Dist: ngs-tools
Requires-Dist: numpy<2.0.0,>=1.21.0
Requires-Dist: pandas
Requires-Dist: polars
Requires-Dist: polars-hash
Requires-Dist: pyaml
Requires-Dist: pyarrow
Requires-Dist: pyfaidx
Requires-Dist: pyfasta
Requires-Dist: pysam
Requires-Dist: pyseq-align
Requires-Dist: regex
Requires-Dist: rich
Requires-Dist: scipy
Requires-Dist: seaborn
Requires-Dist: setuptools-rust
Requires-Dist: tables
Provides-Extra: doc
Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
Requires-Dist: ipykernel; extra == 'doc'
Requires-Dist: ipython; extra == 'doc'
Requires-Dist: myst-nb; extra == 'doc'
Requires-Dist: pandas; extra == 'doc'
Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
Requires-Dist: sphinx-book-theme>=1.0.0; extra == 'doc'
Requires-Dist: sphinx-copybutton; extra == 'doc'
Requires-Dist: sphinx>=4; extra == 'doc'
Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
Requires-Dist: sphinxext-opengraph; extra == 'doc'
Provides-Extra: rs
Requires-Dist: maturin; extra == 'rs'
Requires-Dist: rogtk; extra == 'rs'
Provides-Extra: sc
Requires-Dist: metacells; extra == 'sc'
Requires-Dist: scanpy; extra == 'sc'
Description-Content-Type: text/markdown

# Olivares Genomic toolkit

# Installation
```
git clone git@github.com:tzeitim/ogtk.git
cd ogtk
pip install -e .[sc,doc,rs]
```

Three main modules are supported.

# ltr
Comprehends lineage tracing analysis for bulk and single-cell data a various modalities. It is capable of pre-processing of multi-site lineage reporters such as GESTALT in addition to single-sites, namely shRNA.

# UM
This represents the main workframe for treating with single-molecule data. 

# Utils
Various recipes for anlayising single-cell RNA-seq data
([metacells](https://github.com/tanaylab/metacells) and
[single-cells](https://github.com/scverse/scanpy)) and implements wrappers for
other genomic toolkits such as [bbtools](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/).

---

Migration to [pola-rs](https://github.com/pola-rs) is work in progress but largely supported.


Notes:
If there are problems with missing zlib-devel not found install `pysam` via conda/mamba since zlib-devel cannot be installed using pip.

