Changes in version 2.12.1 o Fix issue in the getData() function when trying to uncompress tar.gz files Changes in version 2.6.2 o Fix issue in the formatData() function. It is now possible to format using fpkm expression values when using Bgee 14.0. o Implementation of regression tests o Update vignette and README Changes in version 2.6.1 o Fix issue on Bgee 14.0 tar.gz annotation file management. o Update README and DESCRIPTION files. Changes in version 2.6.0 o Compatibility with new tar.gz compressed download files. o Better management of potential issues with the ontology structure. o Better management of .RData object datasets used to create the vignette. o Fixed small issue with species names composed of more than 2 names (e.g Canis lupus familiaris). Changes in version 2.3.2 o Compatibility of the TopAnat part of the package with the new Bgee release 14 (www.bgee.org/bgee14/). o Better management of potential issues with the ontology structure. Changes in version 2.3.1 o Compatibility with the new Bgee release 14 (www.bgee.org/bgee14/) only for the processed data download part. o The TopAnat part still temporarily uses data from Bgee release 13.2, until the webservice is ready. o Retro compatibility with Bgee release 13.2 (www.bgee.org/bgee13/). Changes in version 2.2.0 o Instead of returning a topGO-compatible object, topAnat.R now returns an object from the topAnatData class, an extension of topGOdata class from the topGO package. o Fixed small issue with management of data types given as input by the user (dataType argument when creating new Bgee class) o Fixed bug in experiment Id check step. Now accomodates SRA Ids. o Fixed data frames header names that included double dots. o Removed dependency to biomaRt in vignette. Code is still detailed but not run, instead a pre-created gene list object is loaded from the data/ directory. Changes in version 2.0.0 (2016-10-10) o Implemented possibility to deal with different Bgee releases. o Improved storage and versioning of cached files. o Implemented use of API key to query our servers in order to prevent overloading and spamming. o Improved management of downloading errors. o Harmonized the use of a Bgee class object by all functions of the package. For example, loadTopAnatData() now requires an input Bgee class object to specify species, dataType and pathToData arguments. o Added input Bgee class object to output of loadtopAnatData() function. o Created new getAnnotation(), getData() and formatData() independent functions to replace the Bgee class methods get_annotation(), get_data() and format_data(). o In formatData() function, when affymetrix data is used, the "stats" parameter is automatically set to "intensities". o Added possibility to reproduce an analysis offline if all data files were previously downloaded in cache. o Fixed data frames headers including spaces to more convenient headers with spaces replaced by dots. o Harmonized use of camelCase in functions arguments. o Added argument allowing to sort result table in makeTable() function. o Implemented management of TPMs as expression unit in future Bgee releases. o Updated vignette. Changes in version 1.0.3 (2016-08-31) o Update of format_data() function to output an Expression Set object. o Fixed makeTable "FDR" column which was a factor instead of a numeric. o Fixed get_data() and format_data() functions, which did not work when multiple chip types were available for an experiment. Changes in version 1.0.0 (2016-05-03) o Public release of BgeeDB Bioconductor package. Enjoy!