Stephen Kelly
9/24/2016
In this example, I will demonstrate how to use gene differential binding data to create a volcano plot using R and Plot.ly. This dataset was generated by DiffBind during the analysis of a ChIP-Seq experiment. Each entry represents a bound peak that was differentially expressed between groups of samples.
First, install any libraries you might not have, load the Plot.ly library, and load the file containing your differential binding data.
| # This code uses Biopython to retrieve lists of articles from pubmed | |
| # you need to install Biopython first. | |
| # If you use Anaconda: | |
| # conda install biopython | |
| # If you use pip/venv: | |
| # pip install biopython | |
| # Full discussion: |
A personal diary of DataFrame munging over the years.
Convert Series datatype to numeric (will error if column has non-numeric values)
(h/t @makmanalp)
SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
