lwaldron · Oct 3, 2026 · Oct 3, 2026 · Oct 3, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: curatedCRCData
 Type: Package
 Title: Colorectal Cancer Gene Expression Analysis
-Version: 2.45.4
+Version: 2.45.5
 Date: 2026-10-03
 Authors@R: c(
     person("Princy", "Parsana", role = "aut"),
@@ -39,8 +39,12 @@ VignetteBuilder: knitr
 License: Artistic-2.0
 biocViews: 
     ExperimentData,
+    ExpressionData,
     CancerData,
-    ExpressionData
+    ColonCancerData,
+    MicroarrayData,
+    RNASeqData,
+    GEO
 URL: https://github.com/waldronlab/curatedCRCData
 BugReports: https://github.com/waldronlab/curatedCRCData/issues
 BuildResaveData: no

diff --git a/NEWS.md b/NEWS.md
@@ -31,6 +31,15 @@
 * Removed `external_data_store.txt` and `Namespace: auto`; explicit
   NAMESPACE exporting only `curatedCRCData()`.
 
+## DOCUMENTATION AND METADATA
+
+* Repaired UTF-8 transcoding damage ("??" artifacts) in 32 dataset man
+  pages: author names, journal references, and statistical symbols
+  restored (ASCII equivalents).
+* biocViews extended to ColonCancerData, MicroarrayData, RNASeqData, and
+  GEO for better discoverability.
+* Removed the empty FULLVcuratedCRCData_counts.csv placeholder.
+
 # curatedCRCData 2.43.1
 
 * Updated package maintainer to Levi Waldron (<lwaldron.research@gmail.com>).

diff --git a/inst/extdata/FULLVcuratedCRCData_counts.csv b/inst/extdata/FULLVcuratedCRCData_counts.csv
diff --git a/man/GSE11237_eset.Rd b/man/GSE11237_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Auman JT, Church R, Lee SY, Watson MA, Fleshman JW, Mcleod HL.??Celecoxib pre-treatment in human colorectal adenocarcinoma patients is associated with gene expression alterations suggestive of diminished cellular proliferation.??Eur J Cancer??2008 Aug 
+  Experimenter name: Auman JT, Church R, Lee SY, Watson MA, Fleshman JW, Mcleod HL. Celecoxib pre-treatment in human colorectal adenocarcinoma patients is associated with gene expression alterations suggestive of diminished cellular proliferation. Eur J Cancer 2008 Aug 
   Laboratory: Auman, Mcleod 2008 
   Contact information:  
   Title: Celecoxib pre-treatment in human colorectal adenocarcinoma patients is associated with gene expression alterations suggestive of diminished cellular proliferation. 

diff --git a/man/GSE12225.GPL3676_eset.Rd b/man/GSE12225.GPL3676_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oosting J et al.??Integrating chromosomal aberrations and gene expression profiles to dissect rectal tumorigenesis.BMC Cancer??2008 Oct 29 
+  Experimenter name: Lips EH, van Eijk R, de Graaf EJ, Oosting J et al. Integrating chromosomal aberrations and gene expression profiles to dissect rectal tumorigenesis. BMC Cancer 2008 Oct 29 
   Laboratory: Lips,  Morreau 2008 
   Contact information:  
   Title: Integrating chromosomal aberrations and gene expression profiles to dissect rectal tumorigenesis. 

diff --git a/man/GSE12945_eset.Rd b/man/GSE12945_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Staub E, Groene J, Heinze M, Mennerich D et al.??An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types.??J Mol Med (Berl)??2009 Jun 
+  Experimenter name: Staub E, Groene J, Heinze M, Mennerich D et al. An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types. J Mol Med (Berl) 2009 Jun 
   Laboratory: Staub, Rosenthal 2009 
   Contact information:  
   Title: An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types. 

diff --git a/man/GSE13067_eset.Rd b/man/GSE13067_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman M et al.??DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers.??Clin Cancer Res??2008 Dec 15 
+  Experimenter name: Jorissen RN, Lipton L, Gibbs P, Chapman M et al. DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers. Clin Cancer Res 2008 Dec 15 
   Laboratory: Jorissen and Sieber 2008 
   Contact information:  
   Title: DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers. 

diff --git a/man/GSE14095_eset.Rd b/man/GSE14095_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsuda K et al.??Gene expression signature and response to the use of leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients.??Clin Transl Oncol??2011 Jun 
+  Experimenter name: Watanabe T, Kobunai T, Yamamoto Y, Matsuda K et al. Gene expression signature and response to the use of leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients. Clin Transl Oncol 2011 Jun 
   Laboratory: Watanabe, Hashimoto 2008 
   Contact information:  
   Title: Gene expression signature and response to the use of leucovorin, fluorouracil and oxaliplatin in colorectal cancer patients. 

diff --git a/man/GSE14333_eset.Rd b/man/GSE14333_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakash S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009 Dec 15 
+  Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakash S et al. Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer. Clin Cancer Res 2009 Dec 15 
   Laboratory: Jorissen and Sieber 2008 
   Contact information:  
   Title: Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer. 

diff --git a/man/GSE16125.GPL5175_eset.Rd b/man/GSE16125.GPL5175_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobianco P et al.??Integrative approach for prioritizing cancer genes in sporadic colon cancer.??Genes Chromosomes Cancer??2009 Nov 
+  Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobianco P et al. Integrative approach for prioritizing cancer genes in sporadic colon cancer. Genes Chromosomes Cancer 2009 Nov 
   Laboratory: Reid, Pierotti 2009 
   Contact information:  
   Title: Integrative approach for prioritizing cancer genes in sporadic colon cancer. 

diff --git a/man/GSE17536_eset.Rd b/man/GSE17536_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et al.??Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer.??Gastroenterology??2010 Mar 
-  Laboratory: Smith JJ,??Beauchamp RD 2009 
+  Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology 2010 Mar 
+  Laboratory: Smith JJ, Beauchamp RD 2009 
   Contact information:  
   Title: Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. 
   URL:  

diff --git a/man/GSE17537_eset.Rd b/man/GSE17537_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et al.??Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer.??Gastroenterology??2010 Mar 
-  Laboratory: Smith JJ,??Beauchamp RD 2009 
+  Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology 2010 Mar 
+  Laboratory: Smith JJ, Beauchamp RD 2009 
   Contact information:  
   Title: Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. 
   URL:  

diff --git a/man/GSE17538.GPL570_eset.Rd b/man/GSE17538.GPL570_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et al.??Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer.??Gastroenterology??2010 Mar 
-  Laboratory: Smith JJ,??Beauchamp RD 2009 
+  Experimenter name: Smith JJ, Deane NG, Wu F, Merchant NB et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology 2010 Mar 
+  Laboratory: Smith JJ, Beauchamp RD 2009 
   Contact information:  
   Title: Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. 
   URL:  

diff --git a/man/GSE18105_eset.Rd b/man/GSE18105_eset.Rd
@@ -8,7 +8,7 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yoshida T et al.??MUC12 mRNA expression is an independent marker of prognosis in stage II and stage III colorectal cancer.??Int J Cancer??2010 Nov 15 
+  Experimenter name: Matsuyama T, Ishikawa T, Mogushi K, Yoshida T et al. MUC12 mRNA expression is an independent marker of prognosis in stage II and stage III colorectal cancer. Int J Cancer 2010 Nov 15 
   Laboratory: Matsuyama, Sugihara 2009 
   Contact information:  
   Title: MUC12 mRNA expression is an independent marker of prognosis in stage II and stage III colorectal cancer. 

diff --git a/man/GSE21510_eset.Rd b/man/GSE21510_eset.Rd
@@ -2,13 +2,13 @@
 \alias{ GSE21510_eset }
 \docType{data}
 \title{ Clinical significance of osteoprotegerin expression in human colorectal cancer. }
-\description{ This study aimed to identify a novel biomarker or a target of treatment for colorectal cancer (CRC).The expression profiles of cancer cells in 104 patients with CRC were examined using laser microdissection and oligonucleotide microarray analysis. Overexpression in CRC cells, especially in patients with distant metastases, was a prerequisite to select candidate genes. The mRNA expression of candidate genes was investigated by quantitative reverse transcriptase PCR (RT-PCR) in 77 patients as a validation study. We analyzed the protein expression and localization of the candidate gene by immunohistochemical study and investigated the relationship between protein expression and clinicopathologic features in 274 CRC patients.Using microarray analysis, we identified 6 candidate genes related to distant metastases in CRC patients. Among these genes, osteoprotegerin (OPG) is known to be associated with aggressiveness in several cancers through inhibition of apoptosis via neutralization of the function of TNF-related apoptosis-inducing ligand. The mRNA expression of OPG in cancer tissues was significantly higher in patients with distant metastases than those without metastases. Overexpression of OPG protein was associated with significantly worse overall survival and relapse-free survival. Moreover, overexpression of the OPG protein was an independent risk factor for CRC recurrence.Overexpression of OPG may be a predictive biomarker of CRC recurrence and a target for treatment of this disease.??2011 AACR. }
+\description{ This study aimed to identify a novel biomarker or a target of treatment for colorectal cancer (CRC).The expression profiles of cancer cells in 104 patients with CRC were examined using laser microdissection and oligonucleotide microarray analysis. Overexpression in CRC cells, especially in patients with distant metastases, was a prerequisite to select candidate genes. The mRNA expression of candidate genes was investigated by quantitative reverse transcriptase PCR (RT-PCR) in 77 patients as a validation study. We analyzed the protein expression and localization of the candidate gene by immunohistochemical study and investigated the relationship between protein expression and clinicopathologic features in 274 CRC patients.Using microarray analysis, we identified 6 candidate genes related to distant metastases in CRC patients. Among these genes, osteoprotegerin (OPG) is known to be associated with aggressiveness in several cancers through inhibition of apoptosis via neutralization of the function of TNF-related apoptosis-inducing ligand. The mRNA expression of OPG in cancer tissues was significantly higher in patients with distant metastases than those without metastases. Overexpression of OPG protein was associated with significantly worse overall survival and relapse-free survival. Moreover, overexpression of the OPG protein was an independent risk factor for CRC recurrence.Overexpression of OPG may be a predictive biomarker of CRC recurrence and a target for treatment of this disease. (c) 2011 AACR. }
 \usage{data( GSE21510_eset )}
 \format{
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishiguro M et al.??Clinical significance of osteoprotegerin expression in human colorectal cancer.??Clin Cancer Res2011 Apr 15 
+  Experimenter name: Tsukamoto S, Ishikawa T, Iida S, Ishiguro M et al. Clinical significance of osteoprotegerin expression in human colorectal cancer. Clin Cancer Res 2011 Apr 15 
   Laboratory: Tsukamoto, Sugihara 2010 
   Contact information:  
   Title: Clinical significance of osteoprotegerin expression in human colorectal cancer. 

diff --git a/man/GSE21815_eset.Rd b/man/GSE21815_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara K et al.??Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers.??Cancer Res??2011 Oct 15 
-  Laboratory: Mori M,??Mimori K,??Yokobori T 2010 
+  Experimenter name: Kogo R, Shimamura T, Mimori K, Kawahara K et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 2011 Oct 15 
+  Laboratory: Mori M, Mimori K, Yokobori T 2010 
   Contact information:  
   Title: Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. 
   URL:  

diff --git a/man/GSE24549.GPL5175_eset.Rd b/man/GSE24549.GPL5175_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Sveen A,????esen TH,??Rognum TO,??Lothe RA,??Skotheim RI. Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. Genome Med 2011 May 27 
-  Laboratory: Sveen A,????esen TH,??Rognum TO,??Lothe RA,??Skotheim RI 2011 
+  Experimenter name: Sveen A, Agesen TH, Rognum TO, Lothe RA, Skotheim RI. Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. Genome Med 2011 May 27 
+  Laboratory: Sveen A, Agesen TH, Rognum TO, Lothe RA, Skotheim RI 2011 
   Contact information:  
   Title: Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. 
   URL:  

diff --git a/man/GSE24550.GPL5175_eset.Rd b/man/GSE24550.GPL5175_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum TO et al.??Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival.Genome Med??2011 May 27 
-  Laboratory: Sveen A,????esen TH,??Rognum TO,??Lothe RA,??Skotheim RI 2011 
+  Experimenter name: Sveen A, Agesen TH, Nesbakken A, Rognum TO et al. Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. Genome Med 2011 May 27 
+  Laboratory: Sveen A, Agesen TH, Rognum TO, Lothe RA, Skotheim RI 2011 
   Contact information:  
   Title: Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. 
   URL:  

diff --git a/man/GSE2630_eset.Rd b/man/GSE2630_eset.Rd
@@ -8,8 +8,8 @@
 \preformatted{
 experimentData(eset):
 Experiment data
-  Experimenter name: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Garc??Foncillas J,??Labarga A. A gene signature of 8 genes could identify the risk of recurrence and progression in Dukes' B colon cancer patients. Oncol Rep 2007 May 
-  Laboratory: Bandr??E,??Malumbres R,??Cubedo E,??Sola J,??Garc??Foncillas J,??Labarga A 2005 
+  Experimenter name: Bandres E, Malumbres R, Cubedo E, Sola J, Garcia-Foncillas J, Labarga A. A gene signature of 8 genes could identify the risk of recurrence and progression in Dukes' B colon cancer patients. Oncol Rep 2007 May 
+  Laboratory: Bandres E, Malumbres R, Cubedo E, Sola J, Garcia-Foncillas J, Labarga A 2005 
   Contact information:  
   Title: A gene signature of 8 genes could identify the risk of recurrence and progression in Dukes' B colon cancer patients. 
   URL: