DeSciDe
Tool for Unbiased Literature Searching and Gene List Curation
Description
Designed for genomic and proteomic data analysis, enabling unbiased PubMed searching, protein interaction network visualization, and comprehensive data summarization. This package aims to help users identify novel targets within their data sets based on protein network interactions and publication precedence of target's association with research context based on literature precedence. Methods in this package are described in detail in: Douglas et al. (2025) <doi:10.1039/D5MO00160A>. Key functionalities of this package also leverage methodologies from previous works, such as: - Szklarczyk et al. (2023) <doi:10.1093/nar/gkac1000> - Winter (2017) <doi:10.32614/RJ-2017-066>.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (1 non-OK)
package dependencies
Package required but not available: ‘STRINGdb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 20, 2026
examples
Running examples in ‘DeSciDe-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_string_network
> ### Title: Plot STRING Network
> ### Aliases: plot_string_network
>
> ### ** Ex
...[truncated]...
g_db, string_ids, file_directory = tempdir(), export = FALSE)
Error in readPNG(postFormSmart(urlStr, .params = params, .ctype = "raw")) :
libpng error: Not a PNG file
Calls: plot_string_network -> <Anonymous> -> get_png -> readPNG
Execution halted