I see a lot of experimental design that is confounded. Please read this important essay to understand why this must be avoided to have quality results from expensive *-seq experiments.
Confounded designs ruin experiments. Current batch effect removal methods will not save you. If you are designing a large genomics experiments, learn about randomization.
I worked on a project recently looking at tissue-specific nuclease expression. I made this interactive heatmap from the enormous GTEX dataset that looks at just nuclease gene expression (in TPM) across more than 50 tissues in the human body. It’s fun to play around with the interactive plot. This is the way data should be presented in 2017. I used the Plotly Python API for the chart.
Unfortunately, Plotly is now nearly $400/year if you want to use it for anything more than a few charts and there is no free option to keep sensitive research data private. There should be an exception for academic research, but there isn’t as far as I know.