RainCloudPlots: shiny app I created an interactive click interface to easily customize RainCloud plots without writing code.
A tree 400MYA in the making: choosing species for a phylogenetic analysis between zebrafish and human genes As of June of 2018, this is the list of species that have a sequenced genome (at least partially) and I use in phylogenetic and reconciliation analysis focused on investigating genetic evolution between zerbafish and mammals:
Featured Should we trust the zebrafish as a model for human inflammatory diseases? Zebrafish is emerging as a suitable research animal for modelling human diseases, but what is the translational potential of its research to humans?
Updating Gene Ontology mappings using biomaRt This is another small R function to download updated Gene Ontology mappings for a set of Ensembl Gene IDs. I use it to obtain the Gene Ontology categories linked to each gene from the zebrafish Zv10 assembly when performing enrichment of a RNAseq in goseq.
Updating gene length data using ensembldb Here is a small R function to download updated gene lengths for a set on Ensembl Gene IDs. I use it to obtain the length of the genes from the zebrafish Zv10 assembly when performing gene ontology enrichment of an rnaseq in goseq.
Preparing a zebrafish RNAseq for GSEA Recently I had to annotate a rnaseq analysis that was only mapped to Ensembl IDs for an enrichment analysis in GSEA and this is the way in which I am getting the most insightful results on my research.
