News@DEE2

Recent updates

12th November 2018 - Ever wondered how accurate DEE2 data actially is? Well we have just undertaken a simulation study and comparison to GEO deposited data to demonstrate the quality of DEE2 data. More details here.

26th October 2018 - Recently there have been many projects with ≥500 SRA runs, meaning that they have not been readily available from the webserver as one file. In order to address this, I've packages SRA projects with ≥200 SRA run numbers into zip files. Only projects with EVERY run processed successfully by DEE2 are included. These are now available here.

7th October 2018 - QC information is now linked in the search results and available by hovering the mouse over the QC link. Note that all the datasets are currently classified as "PASS" but this will be chenging soon. Also we moved to another nectar server with storage so there have been some updates to webserver cgi scripts. Also the keyword search is now case insensitive.

22nd September 2018 - the bulk data dumps are now available via http. Dat turned out to be too slow and unreliable for files of this size.

21st September 2018 - Several small bits of news. Firstly a new domain name server that is working much better than the last one. Still unable to get https working so this will not likely happen while using Nectar servers. Secondly the domain name sever change broke the docker image so it was modified and rebuilt. Thirdly the data processing is progressing steadily with the torrent of new datasets that became visible upon integration with the newest SRAdbV2. Lastly, the R interface hs undergone several improvements and should be more robust now. The new documentation has been added (link).

14th March 2018 - search functionality has been restored, so feel free to test it out.

1st March 2018 - Hope you like the new mobile friendly webpage

31st January 2018 - DEE2 data pipeline is finalised and processing is underway. For more information, see the recent blog post.

18th October 2017 - As of a month ago, the original DEE site has been down and we've been working towards DEE version 2, which will be hosted by Monash Uni. This app is still under construction, but stay tuned for the official release at the end of 2017.

15th December 2016 - Our lab is moving to Monash Central Clinical School. Stay tuned for a revamped DEE in 2017 with new data and features. This URL could go dead anytime next year so please finalise your work.

13th August 2016 - Looking for Illumina bodymap2 count data? Try searching ERP000546 for human.

13th August 2016 - Bulk data dumps are back online. An issue with the count matrix headers was resolved.

12th August 2016 - Due to an issue with the bulk data dumps, these have been taken down until the problem is resolved. We apologize for the inconvenience.

14th July 2016 - Our analysis servers are undergoing upgrades and the July database update will be delayed by approx 2 weeks.

19th Jan 2016 - More quality control measures are being added to DEE. This will enable users to view basic QC info such as base qualities, number of reads, proportion uniquely mapped, etc. before downloading. These data will be provided to users in parallel with the expression count matrices. Enhanced QC data are already available for E coli, C elegans and A thaliana, but are in progress for other species.

8th Jan 2016 - Ever searched for datasets and got the error "Too many results found"? We've modified the interface to display all search results when over the >500 datasets limit. This should allow users to select accession numbers of interest.

8th Jan 2016 - A bug in the R function has been resolved. If you had trouble with it before, give it another try and let us know if you encounter any issues getting your data into R.

31st Dec 2015 - The latest update run is underway and looking to add about 37k human and 17k mouse datasets. We have all available servers on the job :)

23rd Dec 2015 - We've performed an upgrade to SRAdb integration to release some further datasets that were previously missing. Thanks for your support in 2015 and making it such a successful year. Thanks to your fedback, we're looking forward to a bunch of new features in 2016. Happy holidays, Merry Christmas and a happy/successful year to you all!

20th Oct 2015 - Public announcement of DEE see my blog post.

24th Sept 2015 - As of yesterday our site is public, but still in the testing phase.

26th Aug 2015 - Bulk and query data are now available in .zip format to improve access for windows and mac users.

24th Aug 2015 - Updates to the datasets are now made weekly based on SRAdb entries.

5th Aug 2015 - Metadata formatting has been streamlined with SRAdb integration.

17th Jul 2015 - More data from human, mouse, Arabidopsis, fruitfly and worm have been added.

9th Feb 2015 - The website is under construction.