fixed buggy aliase

sigven · Dec 21, 2024 · 4df289e · 4df289e
1 parent ed5a161
commit 4df289e
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Showing 8 changed files with 52 additions and 8 deletions.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   release:
     types: [published]
   workflow_dispatch:

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,16 @@
+# Version 1.8.8
+
+* Removed buggy drug aliases from PubChem
+* Updated DepMap RNA fusion events (24Q4)
+
 # Version 1.8.7
 
 * NCI Thesaurus update (24.11d)
 * CIViC update (20241218)
 * New custom drug categories
- - ICIs - CTLA4 inhibitors
- - ICIs - TIGIT inhibitors
- - ICIs - LAG3 inhibitors
+  - ICIs - CTLA4 inhibitors
+  - ICIs - TIGIT inhibitors
+  - ICIs - LAG3 inhibitors
 
 # Version 1.8.1
 

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/biomarker_utilities.R b/data-raw/biomarker_utilities.R
@@ -2334,7 +2334,7 @@ load_custom_fusion_db <- function() {
   return(biomarker_items)
 }
 
-load_depmap_fusions <- function(db_datestamp = "24Q2"){
+load_depmap_fusions <- function(db_datestamp = "24Q4"){
 
   # Load DepMap fusions
   depmap_data <- list()

diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -207,7 +207,7 @@ biomarkers[['metadata']] <- metadata$biomarkers
 #  substr(as.character(packageVersion("pharmOncoX")),1,4),
 #  as.character(as.integer(substr(as.character(packageVersion("pharmOncoX")),5,5)) + 1))
 
-version_bump <- "1.8.7"
+version_bump <- "1.8.8"
 
 db <- list()
 db[['biomarkers']] <- biomarkers

diff --git a/data-raw/drug_names_ignore.tsv b/data-raw/drug_names_ignore.tsv
@@ -187,6 +187,45 @@ preconceive
 wintergreen
 vasoconstrictor
 peppermint
-
+autologous
+allogeneic
+emission
+discharge
+compound
+biospecimen
+emulsion
+potassium
+magnesium
+sodium chloride
+suspension
+conjugate
+conjugated
+carbohydrates
+wild-type reovirus
+option.
+designated
+analog
+analogue
+dedicated
+anthracycline
+mouthwash
+buffered
+buffer
+pharmaceuticals
+pharmaceutical agent
+drug substance
+pharmacologic agent
+pharmacologic substance
+therapeutic agent
+polymer
+hydrochloride
+trans
+hormonal
+hormones
+emla
+polymeric
+buffering agent
+clear by design
+cluster of designation
 
 
diff --git a/data-raw/metadata_pharm_oncox.xlsx b/data-raw/metadata_pharm_oncox.xlsx
diff --git a/pkgdown/index.md b/pkgdown/index.md
@@ -17,7 +17,7 @@ releases of external databases:
  - ChEMBL (v34)
  - NCI Thesaurus (24.11d)
  - MitelmanDB (20241015)
- - CIViC (20241218)
+ - CIViC (20241221)
 
 ### Getting started