Changes in version 2.18.2
o Solve issue when downloading all data from one species
Changes in version 2.18.1
o Possibility to retrieve single cell full length RNA-Seq from
Bgee 15.0 and after
o Possibility to filter data based on sex and strain for Bgee
15.0 and after
o Possibility to filter on cellTypeId for single cell full length
RNA-Seq for Bgee 15.0 and after
o Added pValue in the download files
Changes in version 2.14.1
o Solve download timeout with Windows
Changes in version 2.14.0
o Store downloaded data in local SQLite databases
o Add filter options to the getData() function
o Implement functions to delete local SQLite databases
o Update vignette and README
Changes in version 2.13.1
o Fix issue in the getData() function when trying to uncompress
huge tar.gz files (like all human data or GTeX experiment)
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!