# OmnipathR v3.2.0 + New resource: PrePPI + Configuration option to completely disable logging to file + New vignettes: Path reconstruction, and Bioconductor 2021 Workshop + Many minor bugfixes and improvements # OmnipathR v2.99.19 (v3.0.0) + NicheNet pipeline works + Fixed an error which resulted value 1 in the `n_references` columns even for records without references # OmnipathR v2.99.17 + Improved quality filtering of intercell networks # OmnipathR v2.99.16 + Improved API for translate_ids + Quality filtering of intercell networks # OmnipathR v2.99.13 + Functions to access KEGG Pathways + More robust access to UniProt (in case of network failures) # OmnipathR v2.99.11 + Improved downloader backends # OmnipathR v2.99.8 + OBO parser + Gene Ontology access, functions to work with ontology trees + Database manager # OmnipathR v2.99.7 + New interactions query parameter: loops + Fixed many caching bugs # OmnipathR v2.99.6 + All downloaders attempt 3 times + New resources: Human Phenotype Ontology and Gene Ontology annotations # OmnipathR v2.99.0 (2021-03-08) + Many new resources besides OmniPath: BioPlex, ConsensusPathDB, EVEX, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, InWeb InBioMap, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011 + Methods for converting network elements to Bio Model Analyzer (BMA) motifs + NicheNet workflow + Some igraph related methods: finding all paths up to certain length; extracting the giant component of a graph + Caching + Logging + Configuration handling # OmnipathR v1.99.0 (2020-10-03) + New tests + Many little bugfixes + Updated package metadata + Preparation for Bioconductor 3.12 # OmnipathR v1.3.4 (2020-08-04) + License and password handling + Can be directed to different server by options # OmnipathR v1.3.1 (2020-06-05) + Addition of the package website. + Modification of the pdf vignette for an html one. + Major refactoring of functions. + Addition of the intercellular network function. + Modification for the intercellular categories. # OmnipathR v1.1.4 (2020-03-28) + Refactored the `import_annotations` method # OmnipathR v0.99.12 (2019-10-10) + Modification in the separation between genes within a complex (from dash to underscore) # OmnipathR v0.99.0 (2019-10-10) + Submitted to Bioconductor