Protein query identifiers

• Added possibility to use protein accessions (RefSeq, Ensembl) as query identifiers
• Updated KEGG pathway database (20210329), MSigDB (v7.3)

PPI score fix

• Fixed bug: minimum score for PPI interactions (argument to onco_enrich) not propagatated properly

UniProt fix

• fixed bug when query type is uniprot_acc

Query verification

• Added dedicated report section that shows validation status for entries in query list
  • users can see which entries are found, not found (or potentially mapped as alias for gene symbols)
• Removed lower limit of 20 entries in query list
• CancerMine update
• Minor aesthetic adjustments for varying input lengths (plots etc.)

NetPath inclusion

• Inclusion of manually curated signalling pathways from NetPath in pathway enrichment module
• General data updates: EFO, DiseaseOntology, UniProt KB, Open Targets Platform, GENCODE

CORUM improvement

• using local version of CORUM for protein complex retrieval
• remaing of arguments to core functions

Interactive sCNA plots

• New: interactive copy number aberration plots (plotly)
• Added previously omitted elements (disease genesets) from KEGG database

Subcellular figure legend and genes of unknown function

• Added possibility to write analysis output to Excel workbook
• Added option to set minimum confidence level for subcellular structure annotations
• Added figure legend for cellular substructures
• Added section that highlights genes of unknown/poorly defined function
• Data updates
  • CancerMine (January 2021)
  • KEGG (January 2021)
  • WikiPathways (January 2021)

Prognostic associations & cell type/tissue enrichment

• Two new features of the report
  • Cell-type specific and tissue-specific gene expression patterns in target set (TissueEnrich)
  • Prognostic associations between gene expression and survival across tumor types (Human Protein Atlas)
• General data updates (UniProt, Open Targets Platform, WikiPathways, KEGG, GENCODE)

Improved PPI retrieval

• For large querysets (> 200 proteins), retrieval of protein-protein interaction data from STRING is now working more efficiently
• For efficiency (response time etc) and filesize of HTML report, maximum queryset size for oncoEnrichR is now set to 800 genes/proteins (minimum size is still 20)
• wikipathways are updated to August 2020