Python
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.
Why guest posting? I want to write more hands-on tutorials, but I realized:
I am not an expert for every data type. I am too busy to write new ones. So that’s why I started to experiment guest posting!
If you want to do a guest posting in my blog which gets 30k views per month, feel free to contact me on LinkedIn.
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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:
There was a paper on this topic: A New Online Computational Biology Curriculum.
I am going to provide a biased list below (I have read most of the books if not all). I say it is biased because you will see many books of R are from Hadely Wickham. I now use tidyverse most of the time.
Unix I suggest people who want to learn bioinformatics starting to learn unix commands first.
I want to split the PBMC scATAC bam from 10x by cluster id. So, I can then make a bigwig for each cluster to visualize in IGV.
The first thing I did was googling to see if anyone has written such a tool (Do not reinvent the wheels!). People have done that because I saw figures from the scATAC papers. I just could not find it. Maybe I need to refine my googling skills.