Category: bioinformatics

Going from a list of accession numbers to a formatted latex table

I just want to highlight two packages in R that really do something useful. mygene (https://bioconductor.org/packages/release/bioc/html/mygene.html) takes a list of accession numbers and gets back genbank records. This is something I'm always doing. There are probably lots of good ways of doing this. xtable (https://cran.r-project.org/web/packages/xtable/index.html) is a bit more unique. It can take an R … Continue reading Going from a list of accession numbers to a formatted latex table →

RNA-seq – how many replicates?

I think we've discussed this paper before in lab meetings, but just thought I'd pop it here for posterity. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? The authors performed an RNA-seq experiment with 48 replicates per condition, identified the significantly differentially expressed genes, and … Continue reading RNA-seq – how many replicates? →

On the optimal use of methylKit

This is a useful paper from 2017 titled Strategies for analyzing bisulfite sequencing data. It reviews sequencing and alignment approaches, general methylome analysis, differential methylation and annotation, as well as recommending analysis platforms for non-coders. Section 4.1 discusses differential methylation methods, comparing three different methods using a simulated dataset, including as a subset of one method … Continue reading On the optimal use of methylKit →