Articles by radiaj

Fundamentals of R Programming and Statistical Analysis Video Course

February 1, 2017 | radiaj

Here is the link to my new course at PACKT publishing. I apologize in advance for some of their video editing choices but you will definitely learn a lot and be able to work through a variety of practical examples to meet your bioinformatic needs. I will upload the R ... [Read more...]

Simulating genes and counts for DESeq2 analysis

January 31, 2017 | radiaj

Sometimes it is helpful to simulate gene expression data to test code or to see how your results look with simulated values from a particular probability distribution. Here I am going to show you how to simulate RNAseq expression data counts from a uniform distribution with a mininum = 0 and maximum = 1200. [Read more...]

Converting mouse to human gene names with biomaRt package

October 14, 2016 | radiaj

Converting mouse gene names to the human equivalent and vice versa is not always as straightforward as it seems, so I wrote a function to simplify the task. The function takes advantage of the getLDS() function from the biomaRt to get the hgnc symbol equivalent from the mgi symbol. [Read more...]

Creating Annotated Data Frames from GEO with the GEOquery package

August 5, 2016 | radiaj

In this post, we will go over how to use the GEOquery package to download a data matrix (or eset object) directly into R and append specific probe annotation information to this matrix for it to be exported as a csv file for easy manipulation in Excel or spreadsheet tools. ...

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Creating color palettes in R

July 10, 2016 | radiaj

In the R post, we will present how to create your own color palettes and how to work with other palettes such as RColorBrewer, wesanderson and hex codes from www.colorcombos.com for exciting color palettes.

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Converting Gene Names in R with AnnotationDbi

July 4, 2016 | radiaj

There are many ways to convert gene accession numbers or ids to gene symbols or other types of ids in R and several R/Bioconductor packages to facilitate this process including the AnnotationDbi, annotate, and biomaRt packages. In this post, we are going to learn how to convert gene ids ... [Read more...]