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

# Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

## Documentation for package ‘GencoDymo2’ version 1.0.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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