v1.1.0

CHANGELOG

v1.0.9

• Addition of synthetic lethality interactions
• Bug fixing
• Changelog

v1.0.8

• Data updates (MSigDB 7.5.1 etc)
• Code refactoring of query identification
• Code refactoring of data loading

Data re-design

• Data updates: Open Targets Platform, UniProt KB, WikiPathways, CancerMine, TCGA, EFO, Human Protein Atlas
• Re-design of data management in the package, analysis now requires an initial database loading step

v1.0.6

• Addition of new modules
  - Regulatory interactions - DoRothEA
  - Ligand-receptor interactions - CellChatDB
  • Data updates: Open Targets Platform, KEGG, WikiPathways, CancerMine, TCGA, EFO, DiseaseOntology
  • Additional dedicated enrichment plots (GO)
  • Improved target rankings (tissue- and celltype enrichment, regulatory interactions)
  • See complete CHANGELOG

HTML report fix

• bug in previous release regarding HTML report generation - due to missing commits

Determinants of survival in cancer

• Added Z-scores per gene based on recently published data
• Updated KEGG

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)