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GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs


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Version

Install

install.packages('GencoDymo2')

Version

1.0.2

License

GPL (>= 3)

Issues

1

Pull Requests

0

Stars

3

Forks

0

Maintainer

Monah Abou Alezz

Last Published

July 14th, 2025

Functions in GencoDymo2 (1.0.2)

extract_introns

Extract Intron Coordinates from GENCODE Annotations
df_to_fasta

Convert Data Frame to FASTA File
eliminate_redundant_elements

Eliminate Redundant Genomic Elements
extract_ss_motif

Extract Splice Site Motifs for MaxEntScan Analysis (5' or 3')
find_cryptic_splice_sites

Identify Potential Cryptic Splice Sites.
compare_release

Compare Annotation Counts Between Two GENCODE Releases
get_gtf

Download GTF File from the GENCODE Database
get_gff3

Download GFF3 File from the GENCODE Database
classify_exons

Classify Exons by Their Relative Transcript Position
extract_cds_sequences

Extract Coding Sequences (CDS) from GTF Annotations
get_latest_release

Get the Latest Gencode Release Dynamically
load_file

Load a GTF or GFF3 file from GENCODE as a data frame.
extract_element_by_strand

Extract Genomic Elements by Strand
calculate_gc_content

Calculate GC Content of Genomic Features
tiny_example_gtf_files

Tiny example GTF files
assign_splice_sites

Assign intron donor and acceptor splice sites consensus
stat_summary

Generate Summary Statistics for Genomic Elements
spliced_trans_length

Calculate Spliced Transcript Lengths
extract_single_exon

Identify Single-Exon Genes/Transcripts in GENCODE Data