rnalib: a Python-based transcriptomics library

Rnalib is a python library for handling transcriptomics data.

Installation

To install the latest release of rnalib, use the following command:

pip install rnalib

To install the latest version of rnalib from source, use the following command:

pip install git+https://github.com/popitsch/rnalib.git

Quickstart

Please see the rnalib's documentation for more information.

Notebooks

We provide a set of ipython notebooks for demonstrating rnalib's API:

• README.ipynb: basic introduction to rnalib
• AdvancedUsage.ipynb: advanced API usage

We also provide a (growing) set of tutorials for demonstrating rnalib in real-world use cases:

• Tutorial: SLAM-seq time-course data analysis

• Tutorial: Comparison of different gene annotation sets (human and fly)

• Tutorial: Transcriptome annotation with genemunge, archs4 and mygene.info

• Tutorial: CTCF analysis with rnalib and bioframe

• Tutorial: A small analysis of shRNA targets

• We also compare rnalib to other genomics libraries wrt. performance in this RelatedWork notebook.