Package: universalmotif 1.23.0
Benjamin Jean-Marie Tremblay
universalmotif: Import, Modify, and Export Motifs with R
Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Authors:
universalmotif_1.23.0.tar.gz
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universalmotif.pdf |universalmotif.html✨
universalmotif/json (API)
NEWS
| # Install 'universalmotif' in R: |
| install.packages('universalmotif', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bjmt/universalmotif/issues
- ArabidopsisMotif - Arabidopsis motif in 'universalmotif' format.
- ArabidopsisPromoters - Arabidopsis promoters as a 'DNAStringSet'.
- JASPAR2018_CORE_DBSCORES - JASPAR2018 CORE database scores
- examplemotif - Example motif in 'universalmotif' format.
- examplemotif2 - Another example motif in 'universalmotif' format.
- fontDFroboto - Polygon coordinates for plotting letters.
On BioConductor:universalmotif-1.23.0(bioc 3.20)universalmotif-1.22.0(bioc 3.19)
Last updated 2 months agofrom:34eb367844
Exports:add_gapadd_multifreqas.data.frameaverage_iccalc_complexitycalc_windowscbindcolMeanscolnamescolSumscompare_columnscompare_motifsconsensus_to_ppmconsensus_to_ppmAAconvert_motifsconvert_typecount_kletscreate_motifcreate_sequencesenrich_motifsfilter_motifsget_bkgget_consensusget_consensusAAget_kletsget_matchesget_scoresicm_to_ppmlog_string_pvalmake_DBscoresmask_rangesmask_seqsmeme_alphmerge_motifsmerge_similarmotif_peaksmotif_pvaluemotif_rangemotif_rcmotif_scoremotif_treencolnormalizenrowpcm_to_ppmposition_icscoreppm_to_icmppm_to_pcmppm_to_pwmprob_matchprob_match_bkgpwm_to_ppmread_cisbpread_homerread_jasparread_matrixread_memeread_motifsread_transfacread_uniproberequires_updateround_motifrowMeansrownamesrowSumsrun_memesample_sitesscan_sequencesscore_matchsequence_complexityshuffle_motifsshuffle_sequencesshuffle_stringslide_funsubsetsummarise_motifsswitch_alphto_dfto_listtrim_motifsungapupdate_motifsview_logoview_motifswindow_stringwrite_homerwrite_jasparwrite_matrixwrite_memewrite_motifswrite_transfac
Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurlfansifarverGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRcppThreadrlangS4VectorsscalessystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectoryamlzlibbioc
Introduction to "universalmotif"
Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jul 01 2024.Last update: 2021-10-17
Started: 2018-08-19
Introduction to sequence motifs
Rendered fromIntroductionToSequenceMotifs.Rmdusingknitr::rmarkdownon Jul 01 2024.Last update: 2023-03-02
Started: 2018-08-19
Motif comparisons and P-values
Rendered fromMotifComparisonAndPvalues.Rmdusingknitr::rmarkdownon Jul 01 2024.Last update: 2021-10-17
Started: 2019-05-26
Motif import, export, and manipulation
Rendered fromMotifManipulation.Rmdusingknitr::rmarkdownon Jul 01 2024.Last update: 2024-03-05
Started: 2018-08-19
Sequence manipulation and scanning
Rendered fromSequenceSearches.Rmdusingknitr::rmarkdownon Jul 01 2024.Last update: 2024-03-14
Started: 2018-08-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add multi-letter information to a motif. | add_multifreq |
| Arabidopsis motif in 'universalmotif' format. | ArabidopsisMotif |
| Arabidopsis promoters as a 'DNAStringSet'. | ArabidopsisPromoters |
| Compare motifs. | compare_motifs |
| Convert motif class. | convert_motifs convert_motifs,AsIs-method convert_motifs,ICMatrix-method convert_motifs,list-method convert_motifs,matrix-method convert_motifs,Motif-method convert_motifs,MotifList-method convert_motifs,pcm-method convert_motifs,pfm-method convert_motifs,PFMatrix-method convert_motifs,PWM-method convert_motifs,pwm-method convert_motifs,PWMatrix-method convert_motifs,TFFMFirst-method convert_motifs,universalmotif-method convert_motifs,XMatrixList-method |
| Convert universalmotif type. | convert_type |
| Create a motif. | create_motif create_motif,AAStringSet-method create_motif,BStringSet-method create_motif,character-method create_motif,DNAStringSet-method create_motif,matrix-method create_motif,missing-method create_motif,numeric-method create_motif,RNAStringSet-method |
| Create random sequences. | create_sequences |
| Enrich for input motifs in a set of sequences. | enrich_motifs |
| Example motif in 'universalmotif' format. | examplemotif |
| Another example motif in 'universalmotif' format. | examplemotif2 |
| Filter a list of motifs. | filter_motifs |
| Polygon coordinates for plotting letters. | fontDFroboto |
| Calculate sequence background. | get_bkg |
| JASPAR2018 CORE database scores | JASPAR2018_CORE_DBSCORES |
| Create P-value databases. | make_DBscores |
| Merge motifs. | merge_motifs |
| Identify and merge similar motifs within a collection of motifs (or simply cluster motifs). | merge_similar |
| Look for overrepresented motif position peaks in a set of sequences. | motif_peaks |
| Motif P-value and scoring utility | motif_pvalue |
| Get the reverse complement of a DNA or RNA motif. | motif_rc |
| Generate 'ggplot2' motif trees with 'ggtree'. | motif_tree |
| Import CIS-BP motifs. | read_cisbp |
| Import HOMER motifs. | read_homer |
| Import JASPAR motifs. | read_jaspar |
| Import motifs from raw matrices. | read_matrix |
| Import MEME motifs. | read_meme |
| Import universalmotif formatted motifs. | read_motifs |
| Import TRANSFAC motifs. | read_transfac |
| Import UNIPROBE motifs. | read_uniprobe |
| Run MEME from within R. | run_meme |
| Generate binding sites from a motif. | sample_sites |
| Scan sequences for matches to input motifs. | scan_sequences |
| Calculate sequence complexity. | sequence_complexity |
| Shuffle motifs by column. | shuffle_motifs |
| Shuffle input sequences. | shuffle_sequences |
| Switch between DNA and RNA alphabets. | switch_alph |
| Tidy manipulation of motifs. | requires_update tidy-motifs to_df to_list update_motifs |
| Trim motifs. | trim_motifs |
| universalmotif: Motif class. | as.data.frame,universalmotif-method cbind,universalmotif-method colMeans,universalmotif-method colnames,universalmotif-method colSums,universalmotif-method initialize,universalmotif-method ncol,universalmotif-method normalize,universalmotif-method nrow,universalmotif-method rowMeans,universalmotif-method rownames,universalmotif-method rowSums,universalmotif-method show,universalmotif-method subset,universalmotif-method universalmotif universalmotif-class [,universalmotif-method [<-,universalmotif-method |
| universalmotif: Import, Modify and Export Motifs with R | universalmotif-pkg |
| Utility functions. | utilities |
| Motif-related utility functions. | add_gap average_ic compare_columns consensus_to_ppm consensus_to_ppmAA get_consensus get_consensusAA get_matches get_scores icm_to_ppm log_string_pval motif_range motif_score pcm_to_ppm position_icscore ppm_to_icm ppm_to_pcm ppm_to_pwm prob_match prob_match_bkg pwm_to_ppm round_motif score_match summarise_motifs ungap utils-motif |
| Sequence-related utility functions. | calc_complexity calc_windows count_klets get_klets mask_ranges mask_seqs meme_alph shuffle_string slide_fun utils-sequence window_string |
| Plot logos from numeric matrices. | view_logo |
| Plot motif logos. | view_motifs |
| Export motifs in HOMER format. | write_homer |
| Export motifs in JASPAR format. | write_jaspar |
| Export motifs as raw matrices. | write_matrix |
| Export motifs in MEME format. | write_meme |
| Export motifs in universalmotif format. | write_motifs |
| Export motifs in TRANSFAC format. | write_transfac |