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
Package: geokit 0.0.1.9000
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:
geokit_0.0.1.9000.tar.gz
geokit_0.0.1.9000.zip(r-4.7)geokit_0.0.1.9000.zip(r-4.6)geokit_0.0.1.9000.zip(r-4.5)
geokit_0.0.1.9000.tgz(r-4.6-x86_64)geokit_0.0.1.9000.tgz(r-4.6-arm64)geokit_0.0.1.9000.tgz(r-4.5-x86_64)geokit_0.0.1.9000.tgz(r-4.5-arm64)
geokit_0.0.1.9000.tar.gz(r-4.7-arm64)geokit_0.0.1.9000.tar.gz(r-4.7-x86_64)geokit_0.0.1.9000.tar.gz(r-4.6-arm64)geokit_0.0.1.9000.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
Last updated from:84e2754f2e. Checks:12 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 214 | ||
| linux-devel-x86_64 | OK | 212 | ||
| source / vignettes | OK | 274 | ||
| linux-release-arm64 | OK | 207 | ||
| linux-release-x86_64 | OK | 264 | ||
| macos-release-arm64 | OK | 171 | ||
| macos-release-x86_64 | OK | 295 | ||
| macos-oldrel-arm64 | OK | 195 | ||
| macos-oldrel-x86_64 | OK | 422 | ||
| windows-devel | OK | 263 | ||
| windows-release | OK | 198 | ||
| windows-oldrel | OK | 3012 | ||
| wasm-release | FAIL | 140 |
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
Build Your Own GEOmetadb
Last update: 2026-06-08
Started: 2026-01-14
Search GEO
Session Information
Last update: 2026-06-08
Started: 2026-01-14
Download Supplementary File from GEO database
sessionInfo
Last update: 2026-01-23
Started: 2026-01-14
Download and Parse Seires matrix File from GEO database
Session Information
Last update: 2026-01-14
Started: 2026-01-14
Download and Parse SOFT File from GEO database
Session Information
Last update: 2026-01-14
Started: 2026-01-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Chat with GEO metadata using natural language | geo_chat geo_console geo_shiny |
| GEO accession type | geo_gtype |
| Retrieve Series Matrix and Create ExpressionSet | geo_matrix |
| Get the metadata of multiple GEO identities | geo_meta |
| Search GEO database | geo_search |
| Open the GEO landing page in a browser | geo_show |
| Retrieve GEO SOFT file from NCBI GEO | geo_soft |
| Get Supplemental Files from GEO | geo_suppl |
| GEO URL resolver | geo_url |
| Apply log2 Transformation to Expression Data | log_trans log_trans.ExpressionSet log_trans.matrix |
| Parse key-value pairs in the metadata of GEO Sample SOFT file | parse_sample_data parse_sample_data.data.frame parse_sample_data.GEOSeries parse_sample_data.list |
