CHANGES IN VERSION 2.8.0 ------------------------ NEW FEATURES o PCA plots now are correctly generated with fixed coordinates CHANGES IN VERSION 2.6.0 ------------------------ NEW FEATURES o Automatically computing size factors where required o Added progress indication when compiling the report BUG FIXES o Fixed after changes in threejs package o Edited dropdown menu to remove unused green badge o Menus start expanded on the side, again o theme_bw applied when needed, corrected previous behavior OTHER NOTES o Updated citation infos o Slight difference in handling validate/need errors CHANGES IN VERSION 2.2.0 ------------------------ NEW FEATURES o Added Demo data, loadable via demo button BUG FIXES o Plots work now without cutting out points when zooming in OTHER NOTES o Saved reactive values are now exported to dedicate environments (instead of assigning to global) CHANGES IN VERSION 1.99.0 ------------------------- OTHER NOTES o Reflecting the major feature added, will trigger a major version number bump. Welcome soon, pcaExplorer 2.0.0! CHANGES IN VERSION 1.1.5 ------------------------- NEW FEATURES o Automated report generation - template available + editor in the app tab for advance user customization o Support for state saving, in the global environment as well as with binary data o All plots generated can be now exported with the dedicated button o Added confidence ellipse for PCA plot o Added 3d pca plot o Added functions to automatically retrieve the annotation in format ready to use for the app o Added profile explorer function, for plotting behaviour across all samples for subset of genes o Added distribution plots o Added pairwise correlation plot o Added table to enhance readability of the gene finder plot, also by annotating sample names BUG FIXES o Minor typos fixed in the tabs o Added option row.names to read.delim for allowing row names when uploading the data OTHER NOTES o Added extra info in the about section o Instructions and vignette rewritten to reflect new design of the app CHANGES IN VERSION 1.1.3 ------------------------- BUG FIXES o Remove y axis limits to gene boxplots o Fixed: correct labels and colors assignements for genespca CHANGES IN VERSION 1.0.0 ------------------------- OTHER NOTES o Released in Bioconductor 3.3 CHANGES IN VERSION 0.99.1 ------------------------- OTHER NOTES o Changed format of the NEWS file CHANGES IN VERSION 0.99.0 ------------------------- OTHER NOTES o Ready for submission to Bioconductor CHANGES IN VERSION 0.9.0 ------------------------- OTHER NOTES o Added TravisCI integration for both branches o Added appveyor integration - plus badges in the README.md o Code cleanup o Added screenshots for the vignette o Removed some lengthy tests CHANGES IN VERSION 0.8.0 ------------------------- NEW FEATURES o Selection of identifier type available in pca2go OTHER NOTES o MIT license o Added TravisCI integration o Added codecov integration o Enhanced documentation BUG FIXES o Couple of layout fixes CHANGES IN VERSION 0.7.0 ------------------------- NEW FEATURES o Vignette full draft done CHANGES IN VERSION 0.6.4 ------------------------- OTHER NOTES o Updated NEWS file CHANGES IN VERSION 0.6.3 ------------------------- NEW FEATURES o About and Instructions done by now o Added some missing details on the documentations CHANGES IN VERSION 0.6.2 ------------------------- OTHER NOTES o Corrected wordings for (cor)relations of principal components with covariates o Added a couple of checks if correct objects are provided CHANGES IN VERSION 0.6.1 ------------------------- NEW FEATURES o Added function to remove selected samples suspected to be deemed as outliers, in order to see the effect of clustering on the good ones CHANGES IN VERSION 0.6.0 ------------------------- OTHER NOTES o Documentation completed o Examples fully working, cleaned up further a little more. CHANGES IN VERSION 0.5.0 ------------------------- OTHER NOTES o Further steps in direction of R CMD check CHANGES IN VERSION 0.4.0 ------------------------- NEW FEATURES o Added pca2go live functionality CHANGES IN VERSION 0.3.0 ------------------------- NEW FEATURES o Added color palette to choose, and dependent on the samples and factors available/selected CHANGES IN VERSION 0.2.0 ------------------------- NEW FEATURES o Multifactorial exploration completed and adaptable to each dataset CHANGES IN VERSION 0.1.0 ------------------------- NEW FEATURES o Restyling and (re)packaging mostly completed