General tools for genomics and lineage tracing

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  • License: MIT License
  • Author: Pedro Olivares
  • Maintainer: Pedro Olivares
  • Provides-Extra: doc , rs , sc
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Project description

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 and single-cells) and implements wrappers for other genomic toolkits such as bbtools.

Migration to 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.

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  • License: MIT License
  • Author: Pedro Olivares
  • Maintainer: Pedro Olivares
  • Provides-Extra: doc , rs , sc
Classifiers

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