Cancer hallmarks

• fixed a few minor bugs
• added cancer hallmark evidence section

Clean Excel

• Cleaned Excel output

Optional cytosol + recurrent variants

• Added option to onco_enrich that may ignore cytosol as a structure in subcelluar heatmap
• Added interactive table with recurrent somatic variants (TCGA) overlapping query set in the SNVs/InDels section
• Added barplot for subcellular locations
• Added barplot for most significant GO terms enriched in query set
• Revised oncoplots (improved font sizing, also including mutation types)
• Fixed bug in PPI's for query sets with few/none interactions
• Updated datasets: MSigDB/GO/Reactome (MSigDB v7.4), UniProt (2021_02)

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