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Changelog

Source: NEWS.md

geokit (development version)

  • Added three vignettes: case studies for diabetic nephropathy and urothelial cancer meta-analysis workflows, and a geo_chat() guide for LLM-assisted exploration of GEO metadata.
  • Added a public Agent Skills file for AI agents, published with the pkgdown site at https://wanglabcsu.github.io/geokit/skills/geokit/SKILL.md.
  • Fixed parse_sample_data() ignoring its sep argument when parsing characteristic key-value pairs, silently skipping non-contiguous characteristics_ch columns, and crashing on custom fields names without a ch<N> suffix (they now prefix parsed columns with the field name).
  • Fixed plain-FTP downloads (ftp_over_https = FALSE) being deleted and reported as failures after a success-detection regression.
  • Fixed a guaranteed crash in geo_matrix() when a platform annotation download fails, and clarified the error when sample metadata lacks platform_id.
  • CI resolves querychat from the posit-dev R-universe after its CRAN archive; workflows and the skill file keep working unchanged.

geokit 0.0.2

This is the first release of geokit on CRAN.

  • Added a unified interface for resolving, downloading, and parsing NCBI GEO resources, including SOFT files, Series Matrix files, supplementary files, and metadata.
  • Added vectorized GEO accession handling and parallel downloads with progress reporting.
  • Added geo_search() for searching GEO records through NCBI Entrez.
  • Added S4 classes and accessors for working with GEO DataSets, Series, Samples, and Platforms.
  • Added geo_chat(), geo_console(), and geo_shiny() for exploring GEO metadata with natural-language queries.
  • Added a Rust-based backend for fast GEO URL resolution and SOFT parsing.