Version 1.3: Even more features, quality of life changes and bug fixes

A brand new version of the eFP-Seq Browser has dropped!

Version 1.3 includes even more features, more quality of life changes and more bug fixes

New features:

• Users can now generate a share link of their current session
• Users can now compare multiple genes variants of a single sample

Quality of Life changes:

• Updated description and details around read map method
• Changed visibility of the gene variant dropdown selection to make it more clear that it is a selectable option
• Added tooltips to r_pb and PRKM to give more details of how to read that information

Bug fixes:

• Change wording/phrasing to prevent confusion
• Changed bamdata_amazon_links to bamdata_araport11 to prevent confusion with the name
• Optimize data calling
• Optimized and minified SVGs
• Updated landing page to more accurately depict current UI
• Updated help section with new features and updated old images with new UI elements
• Fixed issue which preventing download table as CSV
• Fixed issue with incorrect samples being displayed in the Klepikova data
• Fixed issue with changing gene variants would either load slowly or not load at all
• Fixed issue with giant arrows in Microsoft Edge
• Fixed issue where incorrect RPKM and r_pb would not change during switch variants
• Fixed issue where relative RPKM would not display the correct information
• If a sample has no control data, now uses the median of all samples instead of empty data
• Replaced more http with https

Known issues:

• The IGB links do not work with Google Drive repositories (link to IGB will not appear for Google Drive files till this is fixed)
• Download page as an image does not render SVGs in Microsoft Edge
• Some sorting arrows may not display in Microsoft Edge

Version 1.2: New features, quality of life changes and bug fixes

A new version of the eFP-Seq Browser has dropped!

Version 1.2 which includes the following new features, quality of life changes, and bug fixes:

New features:

• Cookie policy and privacy policy has been added to the landing page when a user arrives
  
• You can now delete your account as a whole which will also delete your uploaded files permanently from the "Manage Account" modal
• Filter eFP images from the RNA-table has been added
  
• Added Klepikova stress data and pollen data to the Klepikova data set
• Switched from samtools' mpileup to bcftools mpileup (samtools mpileup is no longer supported)
• RPKM calculations now exclude introns from its calculations

Quality of Life changes:

• You can now press enter on the locus ID or y-axis scale input boxes to load a data set
• You can now have no input for your read maps or insert 0 to have the eFP-Seq Browser find the read maps count for you
• "araport.cyverse-cdn" is now an alternative option to Amazon's AWS
• Switching between absolute and relative mode no longer requires loading the table again
• Added a hover/tooltip to the loading bar to display how much of the page has been loaded (as a percentage)
• Changed colour of buttons when enabled to more clearly indicate what can be clickable

Bug fixes:

• Add extra verification and security steps to any aspect of the eFP-Seq Browser that involves a user's account
• Spelling mistakes, grammar and styling has been corrected
• Help images and landing page image now more accurately represents the current version of the eFP-Seq Browser
• Simplified some of the cognitive complexity within the open source code and added more documentation
• Updated readmap counts for the Klepikova data and updated BAM index files for all default data sets
• Changed PCC to r_pb to more accurately depict what it is
• Fixed bug where if no XML is selected in "Manage Account", the user was still able to delete XMLs
• Fixed bug where deleted XMLs would stay listed as an option to the user until next refresh
• Fixed bug where the delete XMLs function would be called unnecessarily, even if the "Manage Account" feature was not opened
• Fixed bug where downloading a file as an XML from the "Manage Account" modal would return nothing
• Fixed bug where main (table and landing page) content would disappear at certain resolutions
• Fixed bug where opening and closing the navbar would sometimes cause the main content to disappear
• Fixed bug where the download table as CSV would return an undefined BAM filename
• Fixed bug where submitting data from the generate data module would not do anything
• Fixed bug where custom AWS data was not able to load/mount correctly
• Fixed bug where the y-scale was fixed to either 1 or 0
• Fixed bug in generating the Google drive link for accessing BAM files
• Fixed bug where if the filename of the BAM file is just ".bam", would prevent the user from moving forward in generating data (security reasons)
• Optimized the speed of loading images (and reduce bandwidth requirements for loading the eFP-Seq Browser)
• Optimized memory usage and fixed memory leak problem

Supplementary data

• The use of R functions and command-line tools to compute the correlation between SR34 gene structures and RNA-coverage from a pollen data set has been added

Updated License

• Updated license from GPLv3 to GPLv2

Known issues:

• The IGB links do not work with Google Drive repositories (link to IGB will not appear for Google Drive files till this is fixed)
• Download page as an image does not render SVGs in Microsoft Edge

Version 1.1: Includes new feature and bug fixes

A new version of the eFP-Seq Browser has dropped!

Version 1.1 which includes the following new features and bug fixes:

New features:

• When clicking on an SVG in the eFP Overview, it will now bring the user to that RNA-table's row
• Table sorting arrows now show a direction

Bug fixes:

• Fixed issue where information will not reset on loading new datasets
• Fissue browser compatibility issues where navbar and RNA-table does not appear side-by-side
• Fixed issue where eFP Overview would not load in Microsoft Edge
• Fixed issue on Microsoft Edge where if the user loads a dataset then refreshes the page, new data will not load unless all input fields have had their information re-entered
• Fixed issue where loading private datasets would not load in the correct order
• Fixed issue where navbar footer would randomly pop out if the screen is maximized
• Fixed issue where if the user was not already logged in Google prior to loading the live version, they were not able to log in at all
• Fixed issue where uploading data from the local computer to eFP-Seq Browser without uploading to private account would not work
• Fixed spelling mistakes
• Added details in the help section that correctly matches the current version of the eFP-Seq Browser
• Help card arrows now show the correct direction arrow when opened (or closed)
• UI more responsive to different window resolutions (fixing weird look on some resolutions)
• Reduced cognitive complexity of the code
• Updated metadata and favicon

Known issues:

• After generating new data, scrolling up doesn't work unless the user scrolls down first
• Does not work on Internet Explorer
• Google Drive repos will not work with IGB
• Download page as an image does not render SVGs in Microsoft Edge

The official full release of the eFP-Seq Browser

The official full release of the eFP-Seq Browser is here! You can visit and use it at https://bar.utoronto.ca/eFP-Seq_Browser/ .

Enjoy!