inst/extdata/NEWS.md

In OceaneCsn/DIANE: DIANE

Version changes in DIANE

1.0.1 : DIANE is released

Version at the moment of the official BMC publication (May 26, 2021).

1.0.2 : Minor bug fixes and improvements.

Improvements :

• Citation was added
• Gene IDs can now have blank space round them in the exploration of specific genes profiles
• MDS was removed
• PCA can now handle expression data with 4 or less experimental conditions
• This document was added to the interface in a new tab

Bug fixes :

• Custom annotation/gene information file now allows duplicated genes
• Custom annotation/gene information now can only have columns named label and/or description
• DEA csv download does not require annotations any more

1.0.3 : Minor bug fixes and improvements.

• Fixed error in DAINE's programming interface (wrong value of the defaut "conditions"" argument in normalize function) 22/11/2021
• Used namesapce operator in data import module to speed up loading

1.0.4 : Minor changes, mainly aesthetic, with no impact one DIANE's main functions and backend. Changes are from merging pull request #36 from Alexandre-So.

• Some code based on bootstrap grid system has been rewrite. This avoid the grey (anthracite) background to show up at the bottom of some pages, and improve shinydashboardPlus::box alignment between different dashboard tabs. This also increases a little bit the width of most of the shinydashboardPlus::box.

• Numbers in the DEA table show less digits when displayed in DIANE (up to 10-3). The downloaded table is not affected.

• When a row is clicked in the DEA table, display a popup with RNAseq count associated with the related gene. (Very cool feature, worth the highlight)

• The little loading square position is now based on user screen resolution. The position can still be improved. Used CSS code is in app_ui.R.

• The little help buttons in the import dataset page have been moved to new locations. This can be done for other tabs.

• Add "y axis" scrollbar to some tables which were exceeded screen boundaries in low resolutions.

• Update contact email to new cnrs one.

1.0.5 : Minor changes and update caused by breaking changes in dependency

• rfPerumte was updated and code had to be change to comply with new function names

• The vignette was improved (mention of seed, and rendering adjustements)

1.0.6 Fixes

• Changed url to diane.ipsim.inrae.fr added license to welcome pages

• Fixed cutom gene info file upload in the case of splicing aware gene IDs in expression file

• Fixed not displaying go results for custom org in network communities

• In draw expression levels, genes filtered because of low expression can still be viewed

January 8, 2024 - Fix

Fix a bug with normalization : Normalization was using total count instead of the normalization factors computed by the chosen method.

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.