v4.2-dev * Load csv in R using UTF-8-BOM to deal with BOM marker that windows sometimes adds * Add a warning if no min expression filter is set * Allow renaming of samples * Add topconfects method for DGE, with new visualisation. Only for pairwise comparison * Add header-menu to gene table. Allow copy of sorted/filtered columns to the clipboard * Add option to select normalisation on QC expression plot and RLE plot * Add support for RUVg and RUVs * Make "dev" interface the default * optionally show "variance" column in table if using mds plot 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