I started to learn bioinformatics because I needed to analyze public ChIP-seq data in 2012. That’s how I got to know Shirley Liu’s lab at Dana-Farber Cancer Institute.
And God knows that I would join her group in 2020 for a staff scientist position to lead the CIDC bioinformatic project.
I witnessed the development of many groundbreaking computational tools for genomics in Shirley’s lab. One tool that I found particularly elegant was BETA (Binding and Expression Target Analysis), developed by Su Wang and published in Nature Protocols in 2013.
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The problem df<- data.frame(id = c(1,2,3), value = c('x,y', 'z,w', 'a')) df #> id value #> 1 1 x,y #> 2 2 z,w #> 3 3 a we want to put x,y in the first row into two rows:
1, x
1, y
and put z,w into two rows too.
solution with R There is a neat function separate_rows that does exactly this in tidyr package:
I need a transcript to gene mapping file for Salmon. I am aware of annotation bioconductor packages that can do this job. However, I was working on a species which does not have the annotation in a package format (I am going to use Drosphila as an example for this blog post). I had to go and got the gtf file and made such a file from scratch.
Please read the specifications of those two file formats.
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