NEWS

curatedCRCData 2.43.1

Updated package maintainer to Levi Waldron ([email protected]).
Refactored DESCRIPTION to use standard Authors@R fields, including maintainer ORCID and funding info (NCI 5U24CA180996).
Fixed invalid biocViews categories to strictly use acceptable ExperimentData terms.
Replaced the unnecessary affy dependency with Biobase in the package Suggests and the vignette.
Added a new CITATION file pointing to the 2018 Genome Biology meta-analysis paper (PMID: 30253799).
Initialized Git LFS to properly track .rda and .RData files.
Removed deprecated zzz.R warning.
Converted the vignette to RMarkdown (.Rmd).

Initial release of curatedCRCData, a comprehensive resource for clinically-oriented investigation of the colorectal cancer transcriptome.
It provides clinically-annotated expression data including The Cancer Genome Atlas (TCGA) RNASeqV2 and Agilent mRNA microarray datasets.
Probesets are mapped to official gene symbols using up-to-date maps.
All clinical annotations are hand-curated and machine-checked to ensure consistent syntax and maximum retention of available clinical variables.
ExpressionSet slots are populated with numerous metadata including PubMed IDs, citations, abstracts, study-specific warnings for retractions and duplicated samples, and probeset <--> gene maps.
The package vignette provides examples for selecting patients and datasets based on flexible rules, performing meta-analysis of potential biomarkers, creating publication-ready tables from ExpressionSet metadata, and simple exporting of data tables for non R-users.