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.

Contributing

We highly welcome contributions! Please see our Contributing section for more information.

Citing

If you use rnalib in your research, please cite our paper.