R

How to plot miRNA, gene expression and functional analysis together

This post should show you an easy way to get the following data type integrated into a figure: functional enrichment analysis gene expression data from any technology miRNA expression data from any technology I am using the function isoNetwork from the package isomiRs, that of course is developed by me :) My ego is not that big, it is just I wanted a figure showing that information, and I couldn’t find any at a time, but if you know any, tweet me about it to @lopantano.

Subset of object creates bigger RDA file size than original object

This is a funny story, and I will try to tell you how I realized I don’t know anything about R in 400 words. I work at the Bioinformatic Core at Harvard TH School. People who know us, or collaborate with us, knows that we mainly use bcbio to analyze sequencing data (check it out, super cool tool). Something that we are working on is to load the data after bcbio finishes into R to ease the downstream analysis.

Get colors for your heatmap annotation

This post will show how to configure quickly the colors for the annotation of rows/columns that go on top or on the side of a heatmap. I normally use pheatmap a lot. Recently I discovered ComplexHeatmap. In both cases I spend always sometime changing the colors of the annotations. I ended up coding a function inside my package DEGreport to do that. Given a data.frame with metadata data information will do: