Package: geokit 0.0.2

Yun Peng

geokit: Tools for Accessing and Working with the Gene Expression Omnibus (GEO)

Provides a tidy and fast R interface to the NCBI Gene Expression Omnibus (GEO) database. Functions are included to query, download, and parse GEO metadata and expression data, making it easier to integrate GEO datasets into downstream analyses and workflows.

Authors:Yun Peng [aut, cre]

geokit_0.0.2.tar.gz
geokit_0.0.2.zip(r-4.7-x86_64)geokit_0.0.2.zip(r-4.6-x86_64)geokit_0.0.2.zip(r-4.5-x86_64)
geokit_0.0.2.tgz(r-4.6-x86_64)geokit_0.0.2.tgz(r-4.6-arm64)geokit_0.0.2.tgz(r-4.5-x86_64)geokit_0.0.2.tgz(r-4.5-arm64)
geokit_0.0.2.tar.gz(r-4.7-arm64)geokit_0.0.2.tar.gz(r-4.7-x86_64)geokit_0.0.2.tar.gz(r-4.6-arm64)geokit_0.0.2.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geokit/json (API)

# Install 'geokit' in R:
install.packages('geokit', repos = c('https://wanglabcsu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wanglabcsu/geokit/issues

Pkgdown/docs site:https://wanglabcsu.github.io

On CRAN:

Conda:

rustcargo

5.76 score 6 stars 10 scripts 32 exports 14 dependencies

Last updated from:353fbf0f79. Checks:7 OK, 5 NOTE, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK193
linux-devel-x86_64OK200
source / vignettesOK261
linux-release-arm64OK196
linux-release-x86_64OK197
macos-release-arm64NOTE193
macos-release-x86_64OK3460
macos-oldrel-arm64NOTE2690
macos-oldrel-x86_64NOTE3622
windows-devel-arm64FAIL368
windows-devel-x86_64OK278
windows-release-arm64FAIL372
windows-release-x86_64NOTE232
windows-oldrel-x86_64NOTE243
wasm-releaseFAIL145

Exports:accessionaccession<-columnscolumns<-datatabledatatable<-geo_chatgeo_consolegeo_gtypegeo_matrixgeo_metageo_searchgeo_shinygeo_showgeo_softgeo_supplgeo_urlgplgpl<-gsegse<-gsmgsm<-log_transmetadatametadata<-parse_sample_datarcd_namercd_name<-rcd_typercd_type<-show

Dependencies:askpassclicurldata.tablehttrjsonlitemimeopensslR6rentrezrlangsysXMLxml2

Case Study: Diabetic Nephropathy Meta-Analysis
Introduction | 1. Multi-Strategy Dataset Discovery | 2. Extract Sample Information | 3. Filter by Quality Criteria | 4. Build a Metadata Database | 5. Annotate and Categorize Datasets | 6. Visualization: Dataset Characteristics | Timeline of Dataset Submissions | Sample Size Distribution | Platform Usage Trends | 7. Prepare a Curated Dataset List | 8. Next Steps for Meta-Analysis | Summary | Session Information
Rendered fromcase-diabetic-nephropathy.Rmdusingknitr::rmarkdown

Last update: 2026-10-25
Started: 2026-10-25

Case Study: Urothelial Cancer Expression Analysis
Introduction | 1. Dataset Discovery | 2. Extract and Process Sample Information | 3. Filter Datasets by Quality Criteria | 4. Download Expression Data | 5. Data Transformation | 6. Exploratory Analysis | 6.1 Expression Distribution | 6.2 Principal Component Analysis (PCA) | 6.3 Sample Correlation Heatmap | 6.4 Summary Statistics | 7. Data Integration Considerations | 8. Visualization: Cross-Dataset Comparison | 9. Next Steps | Summary | Session Information
Rendered fromcase-urothelial-cancer.Rmdusingknitr::rmarkdown

Last update: 2026-10-25
Started: 2026-10-25

Chat with GEO Metadata
Prerequisites | Choosing an LLM Client | From Search Results to a Chat Session | From a Metadata Database to a Chat Session | A Self-Contained Example | Session Information
Rendered fromgeo-chat.Rmdusingknitr::rmarkdown

Last update: 2026-10-25
Started: 2026-10-25

Build Your Own GEOmetadb
Search and Filter Single-Cell Studies of Urothelial Carcinoma | 1. Search for Related Series by Keywords (e.g., Bladder/Urothelial Cancer) | 2. Extract Sample Count from the "Contains" Field | 3. Fetch Series Metadata (Parallel Processing and Batch Saving to Local Directory) | 4. Filter Possible Single-Cell Studies (Search for Keywords in Summary/Title/Design) | Session Information
Rendered fromgeometadb.Rmdusingknitr::rmarkdown

Last update: 2026-06-08
Started: 2026-01-14

Search GEO
Session Information
Rendered fromgeo-search.Rmdusingknitr::rmarkdown

Last update: 2026-06-08
Started: 2026-01-14

Download Supplementary File from GEO database
sessionInfo
Rendered fromgeo-suppl.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-14

Download and Parse Seires matrix File from GEO database
Session Information
Rendered fromgeo-matrix.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2026-01-14

Download and Parse SOFT File from GEO database
Session Information
Rendered fromgeo-soft.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2026-01-14