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.

FANTOM5平台提供了成千上万的人类和小鼠样本的高精度数据。此数据的庞大规模可能令人感到压迫，且本地操作存在挑战。幸而，市面上有许多工具可以帮助我们简化工作流程。在创建本教程中可操作的小型数据子集时，我使用了TET：Fantom 5表格提取工具。我选取了若干人类样本，主要是脑组织样本，并附带了少数异常样本，如子宫，并从网站下载了分隔为表的文件。对于更高级的数据提取，查阅TET的API是一个不错的选择。我选取了标准化后的tpm（每百万个标签的标签数）和注释数据，以便我们能够专注于蛋白质编码基因的处理数据。