Downloading through Google Drive can somethis cause trouble due to
downloading limitations issued by Google. As an alternative approach,
one can now download datasets using another host (server hosted by the
University of Oslo), through the argument
googledrive = FALSE in
oncoEnrichR::load_db()
Protein-protein interactions
Users can opt to show isolated nodes (nodes with no interactions) or
not - logical argument to onco_enrich():
ppi_show_isolated_nodes (default FALSE)
Added protein-protein interaction network based on interactions
found in BioGRID
Users can set a minimum required threshold for the number of
evidence items required for each interaction in BioGRID
New numerical argument to onco_enrich():
ppi_biogrid_min_evidence
Users can restrict the STRING network to physical
interactions only or an extended network also including indirect (
functional ) interactions - API
network type
New character argument to onco_enrich():
ppi_string_network_type (physical or
functional)
Previous argument ppi_score_threshold is now named
ppi_string_min_score, with a scale that goes from 0 to 1
(as opposed to 0-1000 in previous versions)
Subcellular compartment annotations
Now using the regularly updated COMPARTMENTS
resource as the underlying source for annotation
Users can set a minimum confidence score for each target compartment
annotation (range from 3 (least confident) to 5 (most confident)), as
well as the required minimum number of channels ( Knowledge,
Text mining or Experimental) that should support a
given target compartment annotation
New arguments to onco_enrich():
subcellcomp_min_confidence,
subcellcomp_min_channels
Annotation of oncogenic/tumor suppressive roles
A revised approach to assign roles as proto-oncogenes or tumor
suppressors is implemented, in which we assign each role with a
confidence level (Moderate/Strong/Very strong) pending upon
support in manually curated resources (Network of Cancer Genes (NCG) or
Cancer Gene Census (CGC)) or support in the biomedical literature
(CancerMine)
Cancer driver annotation
A more conservative approach for driver gene status is implemented:
requiring support from at least two distinct resources (Network
of Cancer Genes (NCG), Cancer Gene Census, TCGA, IntOGen, or
CancerMine)
Argument renaming - Renamed arguments to
onco_enrich() for improved naming consistency:
ppi_string_min_score
ppi_string_network_type
ppi_biogrid_min_evidence
ppi_show_drugs
ppi_show_isolated_nodes
regulatory_min_confidence
enrichment_p_value_cutoff
enrichment_q_value_cutoff
enrichment_p_value_adj
enrichment_plot_num_terms
enrichment_simplify_go
enrichment_max_geneset_size
enrichment_min_geneset_size
subcellcomp_min_confidence
subcellcomp_show_cytosol
subcellcomp_min_channels
Other
added oncoEnrichR favicon to output HTML reports
Version 1.3.2
Date: 2022-09-27
Changed
Cancer driver classification in Cancer associations
section. Driver classification is based on the union of IntOGen
mutational driver catalogue (v2020-02-01) and Network of Cancer Genes
(canonical drivers, v7.0)
Recurrent somatic variants (SNVs/InDels, as found in TCGA) are
appended to Excel output worksheet, tab
RECURRENT_VARIANTS
Fixed
A few erroneous mutation hotspots in
Tumor aberration frequencies section
Changed
Slight modification to column names in
Drug associations section
Added links to ENSEMBL_GENE_ID in
Tumor aberration frequencies section
Version 1.3.0
Date: 2022-09-12
Added
Data updates:
MSigDB (August 2022.1)
Changed
Fixed some artefacts (-AS1 entries) in the output of
CancerMine
Added approved_drugs as a column to the
Drug associations section of the output report
Version 1.2.2
Date: 2022-09-02
Added
Data updates:
WikiPathways (20220810)
KEGG (20220809)
Changed
Now using googledrive as data
repository host, due to unstable code using Zenodo
Version 1.2.1
Date: 2022-07-13
Added
Data updates:
WikiPathways (20220610)
Open Targets Platform (2022.06)
CancerMine (v47)
Version 1.2.0
Date: 2022-06-24
Changed
Moved to zenodo.org for hosting
underlying datasets, accessed with zen4R
MAF objects (TCGA) no longer loaded from GitHub
Function oncoEnrichR::write() now requires the
oncoEnrichR database object (oeDB) as an argument
Version 1.1.1
Date: 2022-06-16
Added
Data updates:
WikiPathways (20220610)
Configurations for onco_enrich() populated at the end
of HTML report
Changed
Option renaming
show_prognostic_cancer_assoc renamed to
show_prognostic.
show_tcga_aberration renamed to
show_aberration
show_regulatory_interactions renamed to
show_regulatory
show_tcga_coexpression renamed to
show_coexpression
Fixed
Bug: database loading missing pfamdb
Relaxed dependency versions (caused conflicts for R versions <
4.2)
Version 1.1.0
Date: 2022-06-10
Added
Data updates:
CancerMine (v46)
Open Targets Platform (2022.04)
WikiPathways (20220510)
GENCODE (v40)
CGC (v96)
TCGA (GDC release 32)
EFO (v42.0)
Module that shows the occurrence of protein domains among query set
members
Protein-complex cancer relevance score
New options
ppi_node_shadow - logical indicating if nodes in the
PPI network should carry a shadow or not
show_domain - logical indicating if report should add
section on protein domain frequencies in query set
Changed
Re-ordering of HTML sections, multiple cosmetic changes
GO enrichment plots: now showing q-value and enrichment factors in
bar plots
Revised method to compute tumor-type specific cancer rank (and
global)
Dedicated output article with output views on
sigven.github.io/oncoEnrichR
Fixed
Bug: duplicate records in retrieved co-expression pairs
Removed most redundant protein complexes in OmniPath
Version 1.0.9
Date: 2022-03-31
Added
Data updates:
CancerMine (v43)
Open Targets Platform (2022.02)
WikiPathways (20220310)
Project Score (July 2021 release)
New analysis section: Synthetic lethality - shows how
members of the queryset overlaps with predicted synthetic lethality
interactions (as published by De Kegel et al., Cell Systems, 2021)
add this section in the output with option
--show_synleth
Fixed
Bug in query identification for background set
Bug in rank of top gene-cancer associations
Changed
Option --show_crispr_lof renamed to
--show_fitness. Corresponding section in HTML report
renamed from CRISPR/Cas9 loss-of-fitness to
Gene fitness scores.
Renamed sections in HTML report:
TCGA co-expression –>
Tumor co-expression
TCGA aberration frequency —>
Tumor aberration frequencies
Sections that include tabsets are now organized so that the
initial active tab always contains data (with the exception of all tabs
being empty)
Version 1.0.8
Date: 2022-02-18
Added
Data updates:
WikiPathways (20220210)
CancerMine (v42)
MSigDB (v7.5.1)
GENCODE (v39)
Gene summary (NCBI)
Reactome/GO (MSigDB v7.5.1)
KEGG (20211223)
Changed
Refactoring of code and data for mapping gene identifiers
Refactoring of code for database loading
Version 1.0.7
Date: 2021-11-30
Added
Data updates
WikiPathways (20211110)
Open Targets Platform (2021.11)
EFO (v3.36.0)
TCGA (v31, 2021-10-29)
CancerMine (v40)
Human Protein Atlas (v21)
UniProt KB (2021_04)
PFAM domains (release 35, November 2021)
Changed
Management of annotation databases have been re-designed, reducing
the size and installation of oncoEnrichR significantly. The
re-design results in the addition of an initial step in the analysis;
database loading.
Explore potential ligand-receptor interactions in the query set, as
found in the CellChat database
Report styling options
Choose your own Bootswatch theme for HTML report - option
html_report_theme
Choose where the table of contents are placed in the HTML report
(floating-left or static at the top) - option
html_floating_toc
Arguments to oncoEnichR::onco_enrich():
html_floating_toc - logical, if set to FALSE, table of
contents in HTML report will be placed on top of the main document
html_report_theme - character, choose between different
Bootswatch themes for style in HTML report
show_regulatory - logical, show regulatory interactions
module (DoRothEA)
min_confidence_reg_interaction - character, minimum
confidence of regulatory interactions included from DoRothEA
(‘A’,‘B’,‘C’, or ‘D’)
show_ligand_receptor - logical, show ligand-receptor
interaction module (CellChatDB)
num_terms_enrichment_plot - integer, number of enriched
Gene Ontology terms (max) to show in enrichment barplots (module
Functional Enrichment)
Default gene rankings
In the modules Regulatory Interactions and
Tissue and cell type enrichment, interactions/targets
are ranked according to a quantitative cancer association score
cancer_max_rank (maximum gene-cancer association rank (Open
Targets Platform) across primary sites)
Fixed
Report disclaimer occurring at the bottom of the report is
no longer missing from web-based analysis (oncotools.elixir.no) - file
_site.yml in inst/templates
