IOBR 2.2.0

CRAN Policy Fix (Resubmission)

• Fixed all functions that wrote to the user’s home filespace (working directory) by default. Writing now only occurs when an explicit path / save_path / output.dir is provided.
• Affected functions: eset_distribution(), find_outlier_samples(), iobr_cor_plot(), sig_pheatmap(), sig_box_batch(), plotPurity(), IPS_calculation(), find_mutations(), sig_gsea(), get_cor(), batch_sig_surv_plot(), format_signatures(), and creat_folder().
• Examples updated to use tempdir() when file writing is demonstrated.

Bug Fixes

• find_mutations(): Fixed semantic naming error where file_name variable was used to store directory paths. Renamed to output_dir for clarity. Fixed ggsave() parameter order issues.
• iobr_cor_plot(): Fixed ggsave() parameter order issues. The correct order is filename first, then plot.
• surv_group(): Fixed ggsave() parameter order issues.
• roc_time(): Fixed ggsave() parameter order issues.
• batch_sig_surv_plot(): Changed default save_path from file.path(tempdir(), "Multiple-KM-plot") to NULL to prevent automatic directory creation.
• format_signatures(): Changed parameter name from output_name to output_path for consistency. Added validation requiring output_path when save_signature = TRUE.
• find_outlier_samples(): Added validation requiring project when save = TRUE.
• plotPurity(): Changed default output.dir from "estimated_purity_plots" to NULL.

Major Changes

• CRAN Size Compliance: Moved large datasets (>5MB total) from R/sysdata.rda and data/ to GitHub Releases to meet CRAN package size requirements. Data is now downloaded on-demand and cached locally.
• New Data Management System:
  • Added load_data() function for unified data access (supports sysdata, exported data, and GitHub-hosted datasets)
  • Added download_iobr_data() with multiple mirror support (GitHub, ghproxy.vip, gh-proxy.org, ghfast.top)
  • Added add_iobr_mirror() for custom mirror configuration
  • Added list_github_datasets() to show available remote datasets
  • Added clear_iobr_cache() to manage downloaded data
• Automatic Caching: Downloaded datasets are cached in user’s cache directory and persist across package updates.
• Fixed count2tpm() to handle symbol-based gene IDs more robustly.

Data Migration

The following datasets are now hosted on GitHub and downloaded on first use: - Reference matrices: BRef, TRef, lm22 - Annotations: anno_gc_vm32, anno_grch38, anno_hug133plus2, anno_illumina, anno_rnaseq - Example datasets: tcga_stad_sig, imvigor210_sig, eset_stad, sig_stad, eset_gse62254, etc. - Gene sets: hallmark, kegg, go_bp, go_cc, go_mf, reactome, msig_immune, msig_sc - Cell markers: cancer_type_genes, cellmarkers, common_genes, immuneCuratedData, ips_gene_set, SI_geneset, mRNA_cell_default, mus_human_gene_symbol, onco_sig, PurityDataAffy - Reference data: xCell.data, quantiseq_data - Signatures: signature_collection_citation, signature_metabolism, signature_sc, signature_tumor

Internal Updates

• Updated all internal code to use load_data() instead of direct object references for migrated datasets
• Updated globalVariables.R to reflect data migration
• Enhanced error messages with manual download instructions when all mirrors fail

IOBR 2.1.1

New Features

• Added Docker support with automated image builds and publishing to GitHub Container Registry (ghcr.io/iobr/iobr). The image is based on rocker/tidyverse and includes IOBR with all dependencies pre-installed (#Docker).
• Added Conda/Mamba installation instructions to README for easier environment setup.
• Expanded iobr_cor_plot() to support multi-group (3+) comparisons using Kruskal-Wallis test, in addition to the existing two-group Wilcoxon test (#28).

Bug Fixes

• Fixed generateRef_DEseq2() to handle sparse single-cell RNA-seq data by using type = "poscounts" for size factor estimation, preventing errors when all genes contain at least one zero.
• Fixed batch_kruskal() output format to correctly display mean-centered values for all groups.
• Fixed count2tpm() computation results to align with previous correct versions.
• Updated count2tpm() documentation to clarify that gene identifiers are converted to gene symbols in the output regardless of input ID type.
• Wrapped some long-running examples in \dontrun{} and \donttest{} to comply with CRAN check time limits.

Improvements

• Refactored internal helper functions in count2tpm.R for better code organization and maintainability.
• Updated load_data() documentation to include additional available datasets.

IOBR 2.1.0

• Initial CRAN submission.