Man pages for bjmt/universalmotif
Import, Modify, and Export Motifs with R
| add_multifreq | Add multi-letter information to a motif. |
| ArabidopsisMotif | Arabidopsis motif in 'universalmotif' format. |
| ArabidopsisPromoters | Arabidopsis promoters as a 'DNAStringSet'. |
| compare_motifs | Compare motifs. |
| convert_motifs | Convert motif class. |
| convert_type | Convert universalmotif type. |
| create_motif | Create a motif. |
| create_sequences | Create random sequences. |
| enrich_motifs | Enrich for input motifs in a set of sequences. |
| examplemotif | Example motif in 'universalmotif' format. |
| examplemotif2 | Another example motif in 'universalmotif' format. |
| filter_motifs | Filter a list of motifs. |
| fontDFroboto | Polygon coordinates for plotting letters. |
| get_bkg | Calculate sequence background. |
| JASPAR2018_CORE_DBSCORES | JASPAR2018 CORE database scores |
| make_DBscores | Create P-value databases. |
| merge_motifs | Merge motifs. |
| merge_similar | Identify and merge similar motifs within a collection of... |
| motif_peaks | Look for overrepresented motif position peaks in a set of... |
| motif_pvalue | Motif P-value and scoring utility |
| motif_rc | Get the reverse complement of a DNA or RNA motif. |
| motif_tree | Generate 'ggplot2' motif trees with 'ggtree'. |
| read_cisbp | Import CIS-BP motifs. |
| read_homer | Import HOMER motifs. |
| read_jaspar | Import JASPAR motifs. |
| read_matrix | Import motifs from raw matrices. |
| read_meme | Import MEME motifs. |
| read_motifs | Import universalmotif formatted motifs. |
| read_transfac | Import TRANSFAC motifs. |
| read_uniprobe | Import UNIPROBE motifs. |
| reexports | Objects exported from other packages |
| run_meme | Run MEME from within R. |
| sample_sites | Generate binding sites from a motif. |
| scan_sequences | Scan sequences for matches to input motifs. |
| sequence_complexity | Calculate sequence complexity. |
| shuffle_motifs | Shuffle motifs by column. |
| shuffle_sequences | Shuffle input sequences. |
| switch_alph | Switch between DNA and RNA alphabets. |
| tidy-motifs | Tidy manipulation of motifs. |
| trim_motifs | Trim motifs. |
| universalmotif-class | universalmotif: Motif class. |
| universalmotif-pkg | universalmotif: Import, Modify and Export Motifs with R |
| utilities | Utility functions. |
| utils-motif | Motif-related utility functions. |
| utils-sequence | Sequence-related utility functions. |
| view_logo | Plot logos from numeric matrices. |
| view_motifs | Plot motif logos. |
| write_homer | Export motifs in HOMER format. |
| write_jaspar | Export motifs in JASPAR format. |
| write_matrix | Export motifs as raw matrices. |
| write_meme | Export motifs in MEME format. |
| write_motifs | Export motifs in universalmotif format. |
| write_transfac | Export motifs in TRANSFAC format. |
