Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

---

Documentation for package ‘GencoDymo2’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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