NEWS.md

OmnipathR v4.0.0

Features

• ID translation ambiguity analysis
• KEGG REST API client
• New metabolomics resources: HMDB, RaMP, Chalmers Sysbio GEMs, STITCH,
• Metabolite-protein interactions from MetalinksDB
• Metabolite ID translation using RaMP and HMDB data

Technical

• Rewritten and improved parameter processing for OmniPath queries
• Rewritten downloaders based on curl and httr2
• Fine control over curl handlers
• Detailed log messages about HTTP requests
• Diagnostic log messages: session info, libraries, versions, platform info, curl options, HTTP timings, headers
• Option to include curl debug log in the log file
• Robust TCP keep-alive parameters that hopefully fix rest.uniprot.org dowloads

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