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- Fixed ncRNA search bar so it is present (under a hamburger menu) at lower window widths, and changed placeholder text to specify mature miRNAs (as opposed to just miRNAs).
- Added some additional mature miRNAs to Atlas census, and removed all precursor miRNAs from Atlas census.
- Now automatically handle (and fix) situation where users put lowercase 'r' in miRNA / piRNA identifiers for ncRNA search bar.
- Added new ncRNA search bar to front page of Atlas (including link in header). Select a ncRNA library (miRNAs, tRNAs, or piRNAs) and a database (Atlas Census), type your ncRNAs of interest, and then click the magnifying glass (or hit enter) to search for those ncRNAs in the selected database.
- Added Atlas Census page to Atlas. Page displays presence of selected ncRNAs in each biofluid in the public Atlas according to various dynamic parameters. User can also perform downstream analysis (Pathway Finder) with selected miRNAs.
- Added new DESeq2 results page. Instead of linking directly to Pathway Finder, page now allows you to see DESeq2 output, select miRNAs of interest, and perform downstream analysis (Pathway Finder) with those selected miRNAs.
- Added My Analyses link to "Browse exRNA Profiles - Alternative Options" panel on front page.
- Added "Return to Default" button for datasets table and stand-alone datasets page.
- Increased font size of dates for news and version history pages.
- Fixed a couple of bugs in FTP data submission pipeline.
- Updated header bar with more obvious link to exRNA Portal.
- Added note to front page about ERCC9 conference.
- Changed symbols associated with each news item.
- Updated faceted charts and bar charts on front page to be slightly larger, and fixed overlapping text issues for certain labels.
- Updated styling for My Analysis Results / Public Analysis Results pages.
- Added Dataset Submissions table to front page.
- Re-arranged header navigation bar and added some new options (like Select Profiles).
- Updated tooltips throughout Atlas to be more accurate and informative.
- Fixed bug related to ERCC Data Policy popup being hidden behind biofluid / assay grid.
- Updated Datasets page and Public Analysis Results page with new features like: better reporting of embargo status (on Datasets page), ascending/descending sorting, load more / load all buttons, and dynamic reporting of number of results currently being displayed.
- Fixed bug related to sorting on datasets page upon page load.
- Updated location of "Sort by" navbar on datasets page, and added checkmark to selected sort method.
- Updated display of atlas statistics on front page to include new samples, datasets, reads, and conditions across different time frames.
- Fixed bug related to user-specific requests.
- Added sorting to Datasets page (via "Sort by" navbar). Page also sorts datasets by sample count (descending) upon page load.
- "Download Dataset Files" popover for each dataset on Datasets page now provides explanatory text alongside each icon. Width is also fixed for this popover so that explanatory text for each icon is formatted properly.
- Fixed borders for all popovers on Datasets page.
- Updated "My Analyses" and "Public Analysis Results" pages by displaying number of analyses per tool, and provided additional description to differentiate "My Analyses" page from "Public Analysis Results" page.
- Added initial support for downloading single qPCR target files via grids (use first icon in "Download Data" column) and updated help text accordingly.
- Fixed a couple of bugs related to loading the Datasets page.
- Fixed a couple of visual bugs related to borders on some of the sample grids.
- Did visual overhaul of all Atlas pages.
- Added usage info at bottom of Datasets page and Analyses page.
- Fixed bug on Linear Tree page by removing animation for floating menubar (still need to fix bug where floating menubar disappears if window is made too narrow).
- Fixed Dimensionality Reduction plots for TPATE1_HEALTHYVSCANCER_ALL, LLAUR1_PLACDYS_ALL, MBITZ1_KIDNEY_ALL, and miRNeasy (biofluids for points were mislabeled).
- Retroactively added an update for version 4.6.5 (2017-05-25) below and on news page (including short news section on front page).
- Added links to version history page from short news section.
- Edited text for short news section to make language more concise (v4.6.5 and v4.6.0 updates).
- Significant overhaul of FTP data submission pipeline to make metadata submission easier (one file per metadata type).
- Improved error reporting for metadata errors (error report more concise and should now usually report all errors in a given file at the same time).
- Added local copies of indices to many computing nodes to ensure faster processing times (and reduce competition between exceRpt jobs).
- User can now give different adapter sequences on a per-sample basis when submitting files to the Atlas.
- Removed animation effect for floating menubar on Atlas homepage, based on user feedback.
- Fixed date for version 4.6.0 update on News page.
- Fixed date for version 4.6.0 update below.
- New RNA-seq dataset added to Atlas: "small RNA Sequencing of Biofluids from Healthy Controls" (PI: Kendall Jensen). Dataset contains 428 profiles and consists of plasma, saliva, and urine samples from healthy college athletes.
- New RNA-seq dataset added to Atlas: "small RNA Sequencing of CSF Samples from Patients with IVH" (PI: Kendall Jensen). Dataset contains 70 profiles.
- Version History page added (available via News page and header's "More" menu).
- Link to News page added to header's "More" menu.