gene annotation database with MongoDB

After reading Datanami’s recent post “9 Must-Have Skills to Land Top Big Data Jobs in 2015” [1], I decided to round out my NoSQL knowledge by learning MongoDB. I have previously reported NoSQL work with Neo4j on this blog, where I discussed building a gene annotation graph database [2]. Here I build a similar gene […]

graph database for gene annotation

Lately I’ve been experimenting with graph databases using Neo4j and the Cypher query language. To get a feel for these tools, I created the following gene annotation network. The Cypher commands I used are discussed in this post, followed by a demonstration of querying the database. Creating the Graph Database We are creating the following […]

comparing mRNA half-life survival curves

In my last post, I illustrated how the Kaplan-Meier estimator can be used to estimate the survival curve of mRNA half-lives. In this post I will expand on that analysis and show how to compare two mRNA half-life Kaplan-Meier curves, each corresponding to a measured gene outcome, to see if mRNA half-life differs between outcomes. […]

mRNA half-life survival curve estimation

In a recent post, I demonstrated the use of the Kaplan-Meier estimator for estimating survival curves of fictional characters undergoing treatment in a fictional drug trial. Here I illustrate the Kaplan-Meier estimator on real data, data that is unique from normal survival analysis data in that the event under consideration is neither time until death […]

werewolf transcriptome conjecture

Lycanthropy—the sudden transformation of individuals into wolf-human chimeras during full moon periods—remains one of the least understood medical conditions persisting today. Researchers find investigation of the phenomenon doubly confounded by social stigma (who wants to tell a scientist that they are a werewolf?) and sampling difficulty (how many werewolves will actually sit still for a […]