topAnat can use the expression calls of Bgee 16. These calls are made in anatomical structures possibly restricted to a cell type
New argument callFileType of loadTopAnatData: the expression calls propagated by Bgee, default from Bgee 16, or the observed ones, that topGO propagates
From Bgee 16, the classic Fisher test, without decorrelation, runs on the propagated calls: BgeeDB computes it itself, without topGO, that would propagate them again, with the same counts and p-values as the classic algorithm of topGO, in seconds rather than minutes for the species with many conditions. termStat, genesInTerm, sigGenes, makeTable and printTopAnatGraph work on its object. The decorrelation algorithms run on the observed calls. Any other combination throws an error
From Bgee 16, topAnat_galaxy runs the classic algorithm on the propagated calls
From Bgee 16, new argument background of topAnat: the gene list is restricted by default to the protein coding genes, downloaded from Bgee; "polyA", "observed" or a vector of gene IDs choose another background. The previous releases are not concerned
New argument foregroundGenes of topAnat, to provide the genes of interest alone instead of a gene list: the gene list is built from the background
From Bgee 16, a Bgee object created without any data type uses the data types of the release
New function printTopAnatGraph, drawing in a PDF file the conditions significant in a topAnat analysis and their ancestors, with their names
makeTable and printTopAnatGraph leave out by default the conditions redundant with a more precise one: those with the numbers of annotated and significant genes and the p-value of one of their sub-conditions. New argument keepRedundant to keep them, makeTable then telling them in a column redundant
loadTopAnatData reports the answer of the server when it refuses a query
loadTopAnatData reads the expression calls faster and with less memory: with fread, and by checking that a download is complete from its last bytes rather than by reading it whole. From Bgee 16, the Bgee API sends the expression calls compressed, and they are kept compressed in the download directory, in a file ending with .tsv.gz
Allows to download data from Bgee 15.2 with more bulk RNA-Seq and single-cell RNA-Seq
Possibility to download h5ad single-cell data with the function getCellProcessedData
Possibility to download integrated Bgee gene expression calls similar to Bgee gene page results with the function getIntegratedCalls
topAnat has been optimized to run faster
The getData function has been deprecated and replaced by the function getSampleProcessedData
Solve issue when downloading all data from one species
Possibility to retrieve single cell full length RNA-Seq from Bgee 15.0 and after
Possibility to filter data based on sex and strain for Bgee 15.0 and after
Possibility to filter on cellTypeId for single cell full length RNA-Seq for Bgee 15.0 and after
Added pValue in the download files
Solve download timeout with Windows
Store downloaded data in local SQLite databases
Add filter options to the getData() function
Implement functions to delete local SQLite databases
Update vignette and README
Fix issue in the getData() function when trying to uncompress huge tar.gz files (like all human data or GTeX experiment)
Fix issue in the formatData() function. It is now possible to format using fpkm expression values when using Bgee 14.0.
Implementation of regression tests
Update vignette and README
Fix issue on Bgee 14.0 tar.gz annotation file management.
Update README and DESCRIPTION files.
Compatibility with new tar.gz compressed download files.
Better management of potential issues with the ontology structure.
Better management of .RData object datasets used to create the vignette.
Fixed small issue with species names composed of more than 2 names (e.g Canis lupus familiaris).
Compatibility of the TopAnat part of the package with the new Bgee release 14 (www.bgee.org/bgee14/).
Better management of potential issues with the ontology structure.
Compatibility with the new Bgee release 14 (www.bgee.org/bgee14/) only for the processed data download part.
The TopAnat part still temporarily uses data from Bgee release 13.2, until the webservice is ready.
Retro compatibility with Bgee release 13.2 (www.bgee.org/bgee13/).
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.
Fixed small issue with management of data types given as input by the user (dataType argument when creating new Bgee class)
Fixed bug in experiment Id check step. Now accomodates SRA Ids.
Fixed data frames header names that included double dots.
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.
Implemented possibility to deal with different Bgee releases.
Improved storage and versioning of cached files.
Implemented use of API key to query our servers in order to prevent overloading and spamming.
Improved management of downloading errors.
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.
Added input Bgee class object to output of loadtopAnatData() function.
Created new getAnnotation(), getData() and formatData() independent functions to replace the Bgee class methods get_annotation(), get_data() and format_data().
In formatData() function, when affymetrix data is used, the "stats" parameter is automatically set to "intensities".
Added possibility to reproduce an analysis offline if all data files were previously downloaded in cache.
Fixed data frames headers including spaces to more convenient headers with spaces replaced by dots.
Harmonized use of camelCase in functions arguments.
Added argument allowing to sort result table in makeTable() function.
Implemented management of TPMs as expression unit in future Bgee releases.
Updated vignette.
Update of format_data() function to output an Expression Set object.
Fixed makeTable "FDR" column which was a factor instead of a numeric.
Fixed get_data() and format_data() functions, which did not work when multiple chip types were available for an experiment.
Public release of BgeeDB Bioconductor package. Enjoy!