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Changelog.txt
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v4.1.1
* Config option to allow skipping header of CSV file
* Config option to allow removing of genes based on regex. eg. use to remove Y-chromomsome from analysis
* Add option under "Extra Settings" to use only samples involved in the comparison
* Add warnings when filters applied to MDS plot
* Add warning when viewing MA-plot or volcano with >2 samples
* Add filtering to "your data" table based on name, and/or description
v4.1.0
* Simple Gene filters added as "Create Filter"
* Experiment can be given a description
* Accept MaxQuant data format to process proteomics data and pre-fill important columns (exprimental)
* QC plots for proteomics added (Imputed value heatmap, Intensity histogram, CV-Histograms)
* Gene table shows intensity or log2 intensity for MaxQuant data
* Gene table can guess UniProt ID lookup when MaxQuant data is loaded (double-click id on gene table)
* Gene table can be searched by comma separating search terms
* Gene table can select columns to show/hide (from cog menu)
* Updated gene-table options and cog
* "View Extra Information" can now display some information in a table
* Moved options to left side of page to always show Strip Chart
* Add button to delete dataset from config page (Under extra options)
* Add button to download R code
* Add button to download a copy of the uploaded counts data (on both View and Config pages)
* Add button to make copy of dataset from "visited" page (split button)
* Heatmap tooltips updated
* Hide irrelevant UI elements on load of "pre-analysed" data
v4.0.0
* Large refactor of front-end to Vue
* Make config page conditions able to be reordered by up/down arrows
* Changing to the MDS tab now sets FDR and FC filters off
* Add analyis mode "logFC only" useful when there are no replicates. Effectively sets p-value to 1
* Add labels and correct colours to 3d MDS, and printing
* Add abitrary contrasts comparison matrix. Configure first, then view on main page.
* Add option for common or independent scaling of the MDS dimensions
* Add selecting older frontend version
v3.2.0
* Add uploading from the command line
* Update docker build. Use specific version of Bioconductor 3.9, so we get predictable R library versions
v3.1.1
* Fix "save to svg" order rendering
* Add sorting to "your data" table
* Add edgeR quasi-likelihood test : https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
* Make gene table able to sort by logFC or abs(logFC)
v3.1.0
* Add printing of MA-Plot
* Add volcano plot
v3.0.0
* New backend in rails
* Allow locking of config by logged-in users
* Add logged-in user info to degust page
v2.1
* Fix CSV downloading in chrome
* Fix handling of files with NA strings
v2.0
* New build with nodejs backend. Rudimentry support for login to track datasets
* Added "save as SVG/PNG" to many plots (right-click)
* Heatmap may show replicates (right-click to select)
* Added colour schemes to heatmap
* Added 3 new QC plots: Library size, expression box-whisker, p-value histogram
* Added gene-expression plot when hovering on table, heatmap or ma-plot
* Download support for CSV, TSV or ODF
v0.21
* Added voomWithQualityWeights option to server version
v0.20
* Add pulldown to select FDR & FC cutoffs
v0.19
* Fix MDS plots. Previously was not normalising for library size.
v0.18
* New condition selector. Better when changing many conditions
* Change to external R templates
* Add selector for DGE method: currently voom/limma or edgeR
v0.17
* Allow linking directly to a plot type using a hash parameter
* Fix bug in labelling of MDS plot when changing condition slection
v0.16
* Fix table search when number column included in table
* Fix bug when '&' used in condition name
* Add title to page
* Rotate heatmap scale so it fits better.
v0.15
* Update heatmap to use web-worker to compute clustering
* Change colours in heatmap, table, kegg to be consistent with red is +ve, blue is -ve
* Add a legend to the heatmap
* Heatmap now ignores the "FC relative to" value. It is always relative to the row average
* Add an MDS plot enabled only when per-replicate count data is available
v0.14
* Option to display counts-per-million instead of raw counts
* Make the parallel-coordinates plot as wide as possible
v0.13
* Add warning to all pages if using IE
v0.12
* Ability to specify count columns in degust.py
* Allow text selection in the gene table
v0.11.2
* Workaround issue with centering of bootstraptour popup.
v0.11.1
* Add axis labels to the MA-plot
v0.11
* Add option to degust.py to load tab-delimitered files
* Add option to degust.py to process cuffdiff output (gene_exp.diff). Note this is still experimental
v0.10.1
* Improve layout on small displays
v0.10
* Make the external URL link used for double-clicking the gene table configurable
v0.9
* Fix log FC filter to use the largest FC between any sample pair
v0.8
* Add script to allow building of a single standalone html
* Add a tour of the site features
* Add loading page when for when pulling down large js
v0.7
* Renamed to "degust" : take the time to appreciate your RNA-seq data...
* Add "show r code" functionality
* Add ability to upload and display user analyed DGE results
* Major code re-organisation to allow combined assets
v0.6
* Changed MA-plot to use canvas. *much snappier*
v0.5
* Added MA-plot
* Better data model handling. Should be easier to support different formats, and
to configure standalone