Man pages for monahton/GencoDymo
Data Extraction and Manipulation from the GENCODE Database
| assign_ss | Assign introns donor and acceptor splice sites consensus |
| classify_exons | Classify exons as single, first, inner or last. |
| eliminate_redundant_exons | Eliminate redundant exons |
| eliminate_redundant_introns | Eliminate redundant introns |
| extract_3ss_motif | Extract the acceptor splice site motif for MaxEntScan web... |
| extract_5ss_motif | Extract the donor splice site motif for MaxEntScan web tool |
| extract_introns | Extract introns coordinates from a GENCODE gtf file as a data... |
| extract_minus | Extract elements on the minus strand from a gtf file. |
| extract_pc | Extract protein-coding genes from GENCODE basic annotation... |
| extract_plus | Extract elements on the plus strand from a gtf file. |
| gencode_compare | Compare number of annotations between 2 different releases... |
| genes_freq | Extract numbers of genes containing single or multiple... |
| load_gtf | Load a gtf file from GENCODE as a data frame. |
| se_genes | Extract single-exon genes |
| se_transcripts | Extract single-exon transcripts |
| spliced_trans_length | Calculate the length of splices transcripts |
| stat_exon | Create a summary statistics table for exons width data |
| stat_intron | Create a summary statistics table for introns width data |
| suppress_output | Suppress the output message of R commands |
| trans_freq | Extract numbers of transcripts containing a single or... |
