Computational biology and genomics
Once upon a time, I made my graphs using Excel because it was the only software that I was aware of for making graphs. Now one can do amazing things with Excel and produce fairly good looking graphs, but after looking at some examples of R graphs, I wanted to learn a bit more about…
After scouring the web all afternoon looking for a solution for visualising gene ontology terms, which I have already found to be over represented, I finally found a simple solution. Prior to this, I had tried several Cytoscape plugins (BiNGO, ClueGO, etc.), online webtools (REVIGO, GOrilla, WEGO, GOLEM, etc.) and others I can’t be bothered…
Once you’ve installed Circos, you can get started with Circos by following the Circos quick guide. Bascially this post was done just by following the guide, which is obviously what you should be looking at; this page just acts as a reminder for myself of what I’ve done. According to the Hello World guide, the…
I’ve written about hierarchical clustering before as an attempt to understand it better. Within R, you can plot the hierarchical clustering results however when working with a large dataset you may produce plots like these where all the labels are overlapping: and As you can see you can’t see any of the labels. During my…
The UCSC Genome Browser provides multiple alignments of 46 vertebrate species and conveniently provides them for download. The multiple alignments show regions of sequence conservation among vertebrates. For more information see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way. The multiple alignments are stored as Multiple Alignment Files and there are Perl and Python packages that parse them. The MAF format is…
A short post about installing Circos on Ubuntu, other Linux distributions and on Windows. Note: if you are using Ubuntu, the location of the env program is in /usr/bin/env. The gddiag and circos programs, use /bin/env, so when you run gddiag it gives a bad interpreter error. Change the first line to #!/usr/bin/perl for both…
First download the relevant tables from here. Download tss_library_expr_summary.tsv.bz2, tss_summary.tsv.bz2 and rna_lib_summary.tsv.bz2 and bunzip2 the files. According to information derived from rna_lib_summary.tsv there are 13,897 CAGE tags from the prostate gland (rna_lib_id = HBA). Double check this: Genomic coordinates of TSSs can be obtained from tss_summary.tsv. Here’s a script which generates bedgraph files of all…
Update 15th May 2018: I recommend using the pheatmap package for creating heatmaps. Heatmaps are great for visualising large tables of data; they are definitely popular in many transcriptome papers. Here are the basic commands for making your own heatmap: The colour schemes from the function display.brewer.all() Returning the values used for the heatmap Taken…