Blog Archives

Fundamentals of R Programming and Statistical Analysis Video Course

February 1, 2017
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Fundamentals of R Programming and Statistical Analysis Video Course

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 code on GitHub and post the links to the...

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Simulating genes and counts for DESeq2 analysis

January 31, 2017
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Simulating genes and counts for DESeq2 analysis

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.

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Converting mouse to human gene names with biomaRt package

October 14, 2016
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Converting mouse to human gene names with biomaRt package

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.

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Creating Annotated Data Frames from GEO with the GEOquery package

August 5, 2016
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Creating Annotated Data Frames from GEO with the GEOquery package

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. This is especially useful for sharing data with collaborators...

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Creating color palettes in R

July 10, 2016
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Creating color palettes in R

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
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Converting Gene Names in R with AnnotationDbi

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 with the AnnotationDbi and org.Hs.eg.db package.

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Working with Venn Diagrams

June 21, 2016
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Working with Venn Diagrams

In this post, we will learn how to create venn diagrams for gene lists and how to retrieve the genes present in each venn compartment with R.

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