Package: GencoDymo2 1.0.4

Monah Abou Alezz

GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

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.

Authors:Monah Abou Alezz [aut, cre, cph], Lorenzo Salviati [ctb], Roberta Alfieri [ctb], Silvia Bione [ctb]

GencoDymo2_1.0.4.tar.gz
GencoDymo2_1.0.4.zip(r-4.7-any)GencoDymo2_1.0.4.zip(r-4.6-any)GencoDymo2_1.0.4.zip(r-4.5-any)
GencoDymo2_1.0.4.tgz(r-4.6-any)GencoDymo2_1.0.4.tgz(r-4.5-any)
GencoDymo2_1.0.4.tar.gz(r-4.7-any)GencoDymo2_1.0.4.tar.gz(r-4.6-any)
GencoDymo2_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GencoDymo2/json (API)

# Install 'GencoDymo2' in R:

install.packages('GencoDymo2', repos = c('https://monahton.r-universe.dev', 'https://cloud.r-project.org'))

Reviews:monahton #

Bug tracker:https://github.com/monahton/gencodymo2/issues

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

On CRAN:

4.78 score 3 stars 6 scripts 444 downloads 18 exports 63 dependencies

Last updated from:98a2f4aba1 (on main). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	393
source / vignettes	OK	328
linux-release	OK	352
macos-release	OK	329
macos-oldrel	OK	246
windows-devel	OK	266
windows-release	OK	247
windows-oldrel	OK	278
wasm-release	OK	203

Exports:assign_splice_sites calculate_gc_content classify_exons compare_release df_to_fasta eliminate_redundant_elements extract_cds_sequences extract_element_by_strand extract_introns extract_single_exon extract_ss_motif find_cryptic_splice_sites get_gff3 get_gtf get_latest_release load_file spliced_trans_length stat_summary

Dependencies:askpass BH BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo cli codetools cpp11 crayon curl data.table dplyr formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue hms httr IRanges jsonlite lambda.r lifecycle magrittr matrixStats mime openssl pillar pkgconfig plotrix prettyunits progress purrr R6 RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Vectors Seqinfo snow stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XML XVector yaml

GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs

Rendered fromGencoDymo2_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-08-21
Started: 2025-04-28

Help page	Topics
Assign intron donor and acceptor splice sites consensus	assign_splice_sites
Calculate GC Content of Genomic Features	calculate_gc_content
Classify Exons by Their Relative Transcript Position	classify_exons
Compare Annotation Counts Between Two GENCODE Releases	compare_release
Convert Data Frame to FASTA File	df_to_fasta
Eliminate Redundant Genomic Elements	eliminate_redundant_elements
Extract Coding Sequences (CDS) from GTF Annotations	extract_cds_sequences
Extract Genomic Elements by Strand	extract_element_by_strand
Extract Intron Coordinates from GENCODE Annotations	extract_introns
Identify Single-Exon Genes/Transcripts in GENCODE Data	extract_single_exon
Extract Splice Site Motifs for MaxEntScan Analysis (5' or 3')	extract_ss_motif
Identify Potential Cryptic Splice Sites.	find_cryptic_splice_sites
Download GFF3 File from the GENCODE Database	get_gff3
Download GTF File from the GENCODE Database	get_gtf
Get the Latest Gencode Release Dynamically	get_latest_release
Load a GTF or GFF3 file from GENCODE as a data frame.	load_file
Calculate Spliced Transcript Lengths	spliced_trans_length
Generate Summary Statistics for Genomic Elements	stat_summary
Tiny example GTF files	tiny_example_gtf_files

Package: GencoDymo2 1.0.4

GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

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