- New resource: PrePPI
- Configuration option to completely disable logging to file
- New vignettes: Path reconstruction, and Bioconductor 2021 Workshop
- Many minor bugfixes and improvements
- NicheNet pipeline works
- Fixed an error which resulted value 1 in the
n_referencescolumns even for records without references
- Improved quality filtering of intercell networks
- Improved API for translate_ids
- Quality filtering of intercell networks
- Functions to access KEGG Pathways
- More robust access to UniProt (in case of network failures)
- Improved downloader backends
- OBO parser
- Gene Ontology access, functions to work with ontology trees
- Database manager
- New interactions query parameter: loops
- Fixed many caching bugs
- All downloaders attempt 3 times
- New resources: Human Phenotype Ontology and Gene Ontology annotations
- 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
- New tests
- Many little bugfixes
- Updated package metadata
- Preparation for Bioconductor 3.12
- License and password handling
- Can be directed to different server by options
- 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.
- Refactored the
import_annotationsmethod
- Modification in the separation between genes within a complex (from dash to underscore)
- Submitted to Bioconductor