Showing posts from January, 2021

DEE2 projects on demand

We have noted that the time between new datasets appearing on SRA and being processed by DEE2 has been about 3 to 6 months. Our dream is to shrink this down to two weeks, but we simply do not have access to that much compute power at the moment. To address this we have devised an "on-demand" feature so that you can request certain datasets to be processed rapidly. We think this is a great feature because it serves the main mission of the DEE2 project which is to make all RNA-seq data freely available to everyone.  Here's how to use it:  1. Visit  and you will be greeted with a webform. Select the organism of interest. 2. Provide the SRA project accession number of the dataset. These numbers begin in SRP/ERP/DRP. If you have a different type of accession such as GEO Series (GSE) or Bioproject (PRJNA) then you will need to navigate NCBI  to find the SRP number.  3. Check that the SRP number is in the standard DEE2 queue. To do that, follow the l

Effect of COVID-19 on genomics publications in 2020

COVID-19 was and remains a major crisis in many countries, disrupting general life as well as scientific research. But how has it impacted scientific output in genomics? To evaluate this I investigated the number of papers published in PubMed Central  (PMC) in the period from 2016 through 2020. I used total number of papers as well as those matching the genomics search term with the approach below: (genom*[Abstract]) AND ("2020"[Publication Date] : "2020"[Publication Date])  <Note: the number of papers is only a lagging proxy measure of aggregate activity in a field, it does not relate to scientific quality> Here are the number of papers and genomics papers published annually over this period. What you can see is that genomics experienced a major fall in number of papers appearing in PMC in 2020 while total papers did not. Indeed 2020 was the only year since 2000 that the number of published genomics papers has actually gone down compared to the previous year