Bioinformatics notebook for Plot.ly
FANTOM5 provides high precision data of thousands of human and mouse samples. The vastness of this data can be overwhelming and operating it locally is challenging. Luckily, there are many tools out there to make our life easier.
For creating a small data subset we can work with in this tutorial, I used TET: Fantom 5 Table Extraction tool. I picked a few human samples, mostly brain tissues with a few outliers, like uterus and downloaded a tab-separated file from the website. For more advanced data extraction, it's good to have a look atTET's API. I have picked normalized tpm(tags per million) and annotated data, so we can focus only on processed data for protein coding genes.