Changelog

Source: NEWS.md

curatedCRCData 2.43.1

  • Updated package maintainer to Levi Waldron ().
  • 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).

curatedCRCData 1.0.0

  • 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.