In the different RNA-Seq experiments, we have found that some experiments have more significant DE (differential expression) genes than others. Besides the experiment design which is the most important factor, a number of other factors may influence the number of DE genes. Here, we list the different experiments that we have carried out the investigation […]
Read MoreWe have recently written a review article entitled “Bioinformatics tools to analyse viral genomics data” for the OIE. In the review, we were unable to provide direct hyperlinks and references to all available tools, simply because there are too many, so we included them here. These commonly used bioinformatics tools are split into the following categories: […]
Read MoreHere are my slides from the BBSRC WestBio DTP skills training session at University of Glasgow, Friday 26th June 2015. The talk was entitled “Case studies of HTS applications” and presents a number of case studies on the application on high-throughput sequencing (HTS), also known as next generation sequencing (NGS), to biological problems ranging from human […]
Read MoreA few days back I posted a question on BioStars about getting genome accession numbers for a list of protein GIs. I had a long list of protein GI and I wanted the genome accession number for each protein GI (if there is one in NCBI databases) but without downloading files for each protein GI […]
Read MoreHere are the slides of my talk in Saskatoon if anybody is interested. The Saskatchewan, like the Glaswegians, are friendly but sometimes hard to understand. They certainly have trouble understanding me. [slideshare id=49505335&doc=oiepresentation-150617124835-lva1-app6891]
Read MoreThe bioinformatics work includes the gene annotation work. In recent years more and more biological data has become available. Meanwhile, how to get the access these valuable data resources and analyse the data is important for comprehensive bioinformatics data analysis. The biomaRt is a very useful tool to achieve that. Now there are two questions: […]
Read MoreIn Computer Science, a trie is a data structure that is also known as a digital search tree or a prefix tree. It can be used for fast retrieval on large data sets such as looking up words in a dictionary. The term trie was invented from the phrase ‘Information Retrieval’ by Fredkin(1960). As a […]
Read More