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Changelog

Source: NEWS.md

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