Computational biology and genomics
I was going to write a post on using the Seurat alignment method as a batch correction tool but as it turned out the two datasets that I chose didn’t seem to have strong batch effects! I heard about the alignment method sometime last year but was motivated to try it out after listening to…
From the original paper describing the Gene Set Enrichment Analysis: The goal of GSEA is to determine whether members of a gene set S tend to occur toward the top (or bottom) of the list L, in which case the gene set is correlated with the phenotypic class distinction.
The Variant Effect Predictor (VEP) tool can be used for annotating variants with respect to custom annotation sources. This is useful if gene models of interest are not represented in the Ensembl or RefSeq databases. To get started, first install VEP since it takes some time.