Counting Transcripts is a Jupyter notebook tutorial series for helping introduce the basics of analyzing cell transcriptome and different tools biologists use when looking at gene expression.

There are four parts of this tutorial:

1. Introduction: setup and basic concepts
2. Pipeline A: Trimmomatic, STAR, cufflinks pipeline
3. Pipeline B: Trimmomatic, kallisto pipeline
4. Extension: application to a real research paper, analyze differentially expressed transcripts with PCA and t-SNE

This tutorial is built for anybody to freely use and download. No prior knowledge is necessary, but it may be helpful to understand cell biology to easier grasp concepts.

Contributors: Andrew Liu, Adrian Lopez Garcia de Lomana, Claudia Ludwig