Man pages for GencoDymo2
Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs
| 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 |
