GencoDymo2
Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs
Description
A comprehensive suite of helper functions designed to facilitate the analysis of genomic annotations from the 'GENCODE' database <https://www.gencodegenes.org/>, supporting both human and mouse genomes. This toolkit enables users to extract, filter, and analyze a wide range of annotation features including genes, transcripts, exons, and introns across different 'GENCODE' releases. It provides functionality for cross-version comparisons, allowing researchers to systematically track annotation updates, structural changes, and feature-level differences between releases. In addition, the package can generate high-quality FASTA files containing donor and acceptor splice site motifs, which are formatted for direct input into the 'MaxEntScan' tool (Yeo and Burge, 2004 <doi:10.1089/1066527041410418>), enabling accurate calculation of splice site strength scores.
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CRAN Check Status
Show all 14 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-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | ERROR |
| 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 (2 non-OK)
package dependencies
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
package dependencies
Packages required and available but unsuitable versions: 'Biostrings', 'GenomicRanges', 'rtracklayer', 'IRanges' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
Check History
ERROR 12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
package dependencies
Packages required and available but unsuitable versions: 'Biostrings', 'GenomicRanges', 'rtracklayer', 'IRanges' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.