Tools

Here you will find code that I use on a regular basis and guides that I think would be of value to the scientific community.
Knick Knacks, code from this site on GitHub Posted March 28th, 2016 I created a GitHub repository for the code on this site Continue reading
CDF plots and mislabeled samples Posted March 21st, 2016 In this post I provide code for making CDF plots with Python and explain how this can be used to check if RNAi microarray samples have been mislabeled. Continue reading
Guide to TCGA data Posted Feb. 28th, 2016 This guide goes over TCGA data, including naming conventions, data restrictions, available data portals, how to download, and potential pitfalls. Continue reading
How to correctly write files with python Posted Feb. 17th, 2016 Writing files with Python may seem simple, but as your data structures become more complex it can be difficult to save the data to file in a way that can be parsed error free. This post describes the easiest and safest method of writing and reading python files. Continue reading
PAR-CLIP: explanation of method and uses Posted Feb. 17th, 2016 PAR-CLIP is a very powerful method for studying RNA-binding proteins and the RNAs they interact with, but researchers may not be aware of this technique or how they can utilize the technique in their research. Continue reading
How to download small RNA-Seq data and find adaptors de novo Posted August 6th, 2015 For someone not experienced in bioinformatics, it is not clear how to search for small RNA-Seq data sets and what are the best methods for downloading them. Unfortunately, downloading the data is only the beginning of the battle. Continue reading
How to download and parse NCBI Nucleotide data Posted August 6th, 2015 NCBI Nucleotide contains a wealth of information that would be useful for almost any scientist, however the data is not parser friendly and it is unclear how to download all the genes of interest. Continue reading
How to make beautiful Kaplan-Meier plots Posted August 6th, 2015 Kaplan-Meier plots are ubiquitous in survival analyses, but it is difficult to find software that will produce publication quality plots. Here I will discuss Kaplan-Meier plots and provide code for plotting them with pylab. Continue reading
A site by Jordan Anaya