The bigmemory package in combination with doMC provides at least a partial solution for sharing a large data set across multiple cores in R. With this solution you can work on the same matrix using several threads. It is also a very scalable solution. ... [Read more...]

One approach for analyzing RNASeq data from an organism with a well-annotated genome, is to align the reads to mRNA (cDNA) sequences instead of the genome. To do that you need to extract the transcript sequences from a database. This is how to extract ensembl transcript sequences from UCSC from ... [Read more...]