{ "_id": "6a1b53ca1d7bb097a0a1140f", "Package": "universalmotif", "Title": "Import, Modify, and Export Motifs with R", "Version": "1.31.32", "Authors@R": "c(\nperson(c(\"Benjamin\", \"Jean-Marie\"), \"Tremblay\", role = c(\"aut\", \"cre\"),\nemail = \"benjamin.tremblay@uwaterloo.ca\",\ncomment = c(ORCID = \"0000-0002-7441-2951\")),\nperson(\"Spencer\", \"Nystrom\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1000-1579\"))\n)", "URL": "https://bioconductor.org/packages/universalmotif/", "BugReports": "https://github.com/bjmt/universalmotif/issues", "Description": "A comprehensive toolkit for working with sequence motifs\nin R. Imports and exports most common motif formats (JASPAR,\nMEME, HOMER, TRANSFAC, CIS-BP, UNIPROBE) and interoperates with\nthe other Bioconductor motif packages. Analysis functions cover\nde novo motif discovery, motif-vs-motif comparison and\nclustering, P-value calculation, sequence scanning, enrichment\nagainst shuffled or composition-matched backgrounds, positional\nbias testing, and pairwise motif co-occurrence. Also includes\nutilities for sequence shuffling, motif trimming, higher-order\nrepresentations, ground-truth simulation by motif implantation,\nand logo-plotting functionality.", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "MotifAnnotation, MotifDiscovery, DataImport, GeneRegulation", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE, old_usage = TRUE)", "Language": "en-GB", "Collate": "'RcppExports.R' 'add_multifreq.R' 'compare_motifs.R'\n'compare_motifs2.R' 'universalmotif-class.R' 'convert_motifs.R'\n'convert_type.R' 'create_motif.R' 'create_sequences.R' 'data.R'\n'dedup_hits.R' 'enrich_motifs.R' 'enrich_motifs2.R'\n'filter_motifs.R' 'get_bkg.R' 'implant_motifs.R'\n'make_DBscores.R' 'match_bkg.R' 'merge_motifs.R'\n'merge_motifs2.R' 'merge_similar.R' 'merge_similar2.R'\n'motif_coocc.R' 'motif_finder.R' 'motif_peaks.R'\n'motif_pvalue.R' 'motif_rc.R' 'motif_tree.R' 'motif_tree2.R'\n'read_cisbp.R' 'read_homer.R' 'read_jaspar.R' 'read_matrix.R'\n'read_meme.R' 'read_motifs.R' 'read_transfac.R'\n'read_uniprobe.R' 'run_meme.R' 'sample_sites.R'\n'scan_sequences.R' 'scan_sequences2.R' 'sequence_complexity.R'\n'shuffle_motifs.R' 'shuffle_sequences.R' 'switch_alph.R'\n'trim_cwm.R' 'trim_motifs.R' 'universalmotif-methods.R'\n'universalmotif.R' 'universalmotif_df.R' 'utils-internal.R'\n'utils-motif.R' 'utils-sequence.R' 'view_logo.R'\n'view_motifs.R' 'view_motifs2.R' 'write_homer.R'\n'write_jaspar.R' 'write_matrix.R' 'write_meme.R'\n'write_motifs.R' 'write_transfac.R' 'zzz.R'", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-30 15:08:17 UTC", "RemoteUrl": "https://github.com/bioc/universalmotif", "RemoteRef": "HEAD", "RemoteSha": "d32921e61f9ad6d59db21b4b6a3fb15083668b13", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 21:01:37 UTC", "User": "root" }, "Author": "Benjamin Jean-Marie Tremblay [aut, cre] (ORCID:\n),\nSpencer Nystrom [ctb] (ORCID: 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"topics": [ "compare_motifs" ] }, { "page": "compare_motifs2", "title": "Faster minimalist motif comparison.", "topics": [ "compare_motifs2" ] }, { "page": "convert_motifs", "title": "Convert motif class.", "topics": [ "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" ] }, { "page": "convert_type", "title": "Convert universalmotif type.", "topics": [ "convert_type" ] }, { "page": "create_motif", "title": "Create a motif.", "topics": [ "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" ] }, { "page": "create_sequences", "title": "Create random sequences.", "topics": [ "create_sequences" ] }, { "page": "dedup_hits", "title": "Deduplicate overlapping motif hits.", "topics": [ "dedup_hits" ] }, { "page": "enrich_motifs", "title": "Enrich for input motifs in a set of sequences.", "topics": [ "enrich_motifs" ] }, { "page": "enrich_motifs2", "title": "Fast minimalist motif enrichment.", "topics": [ "enrich_motifs2" ] }, { "page": "examplemotif", "title": "Example motif in 'universalmotif' format.", "topics": [ "examplemotif" ] }, { "page": "examplemotif2", "title": "Another example motif in 'universalmotif' format.", "topics": [ "examplemotif2" ] }, { "page": "filter_motifs", "title": "Filter a list of motifs.", "topics": [ "filter_motifs" ] }, { "page": "fontDFroboto", "title": "Polygon coordinates for plotting letters.", "topics": [ "fontDFroboto" ] }, { "page": "get_bkg", "title": "Calculate sequence background.", "topics": [ "get_bkg" ] }, { "page": "implant_motifs", "title": "Implant sampled motif instances into sequences at known positions.", "topics": [ "implant_motifs" ] }, { "page": "JASPAR2018_CORE_DBSCORES", "title": "JASPAR2018 CORE database scores", "topics": [ "JASPAR2018_CORE_DBSCORES" ] }, { "page": "make_DBscores", "title": "Create P-value databases.", "topics": [ "make_DBscores" ] }, { "page": "match_bkg", "title": "Sample composition-matched background sequences from a universe.", "topics": [ "match_bkg" ] }, { "page": "merge_motifs", "title": "Merge motifs.", "topics": [ "merge_motifs" ] }, { "page": "merge_motifs2", "title": "Merge a list of motifs into a single consensus motif.", "topics": [ "merge_motifs2" ] }, { "page": "merge_similar", "title": "Identify and merge similar motifs within a collection of motifs (or simply cluster motifs).", "topics": [ "merge_similar" ] }, { "page": "merge_similar2", "title": "Cluster similar motifs by significance and merge each cluster.", "topics": [ "merge_similar2" ] }, { "page": "motif_coocc", "title": "Find significantly co-occurring motif pairs in a set of sequences.", "topics": [ "motif_coocc" ] }, { "page": "motif_finder", "title": "Discover _de novo_ motifs in a set of sequences.", "topics": [ "motif_finder" ] }, { "page": "motif_peaks", "title": "CentriMo-style positional enrichment of motif hits.", "topics": [ "motif_peaks" ] }, { "page": "motif_pvalue", "title": "Motif P-value and scoring utility", "topics": [ "motif_pvalue" ] }, { "page": "motif_rc", "title": "Get the reverse complement of a DNA or RNA motif.", "topics": [ "motif_rc" ] }, { "page": "motif_tree", "title": "Generate 'ggplot2' motif trees with 'ggtree'.", "topics": [ "motif_tree" ] }, { "page": "motif_tree2", "title": "Generate ggtree-based motif trees using 'compare_motifs2()'.", "topics": [ "motif_tree2" ] }, { "page": "plot_match_bkg", "title": "Visualise composition match between target and background sequences.", "topics": [ "plot_match_bkg" ] }, { "page": "plot_motif_peaks", "title": "Plot the position distribution of motif hits.", "topics": [ "plot_motif_peaks" ] }, { "page": "read_cisbp", "title": "Import CIS-BP motifs.", "concept": [ "read_motifs" ], "topics": [ "read_cisbp" ] }, { "page": "read_homer", "title": "Import HOMER motifs.", "concept": [ "read_motifs" ], "topics": [ "read_homer" ] }, { "page": "read_jaspar", "title": "Import JASPAR motifs.", "concept": [ "read_motifs" ], "topics": [ "read_jaspar" ] }, { "page": "read_matrix", "title": "Import motifs from raw matrices.", "concept": [ "read_motifs" ], "topics": [ "read_matrix" ] }, { "page": "read_meme", "title": "Import MEME motifs.", "concept": [ "read_motifs" ], "topics": [ "read_meme" ] }, { "page": "read_motifs", "title": "Import universalmotif formatted motifs.", "concept": [ "read_motifs" ], "topics": [ "read_motifs" ] }, { "page": "read_transfac", "title": "Import TRANSFAC motifs.", "concept": [ "read_motifs" ], "topics": [ "read_transfac" ] }, { "page": "read_uniprobe", "title": "Import UNIPROBE motifs.", "concept": [ "read_motifs" ], "topics": [ "read_uniprobe" ] }, { "page": "run_meme", "title": "Run MEME from within R.", "topics": [ "run_meme" ] }, { "page": "sample_sites", "title": "Generate binding sites from a motif.", "topics": [ "sample_sites" ] }, { "page": "scan_sequences", "title": "Scan sequences for matches to input motifs.", "topics": [ "scan_sequences" ] }, { "page": "scan_sequences2", "title": "Minimalist motif scanner aligned with yamtk scan defaults.", "topics": [ "scan_sequences2" ] }, { "page": "sequence_complexity", "title": "Calculate sequence complexity.", "topics": [ "sequence_complexity" ] }, { "page": "shuffle_motifs", "title": "Shuffle motifs by column.", "topics": [ "shuffle_motifs" ] }, { "page": "shuffle_sequences", "title": "Shuffle input sequences.", "topics": [ "shuffle_sequences" ] }, { "page": "switch_alph", "title": "Switch between DNA and RNA alphabets.", "topics": [ "switch_alph" ] }, { "page": "tidy-motifs", "title": "Tidy manipulation of motifs.", "topics": [ "requires_update", "tidy-motifs", "to_df", "to_list", "update_motifs" ] }, { "page": "trim_cwm", "title": "Trim CWM motifs by absolute column sum.", "topics": [ "trim_cwm" ] }, { "page": "trim_motifs", "title": "Trim motifs.", "topics": [ "trim_motifs" ] }, { "page": "universalmotif-class", "title": "universalmotif: Motif class.", "topics": [ "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" ] }, { "page": "universalmotif-pkg", "title": "universalmotif: Import, Modify and Export Motifs with R", "topics": [ "universalmotif-package", "universalmotif-pkg" ] }, { "page": "utilities", "title": "Utility functions.", "topics": [ "utilities" ] }, { "page": "utils-motif", "title": "Motif-related utility functions.", "topics": [ "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" ] }, { "page": "utils-sequence", "title": "Sequence-related utility functions.", "topics": [ "calc_complexity", "calc_windows", "count_klets", "get_klets", "mask_ranges", "mask_seqs", "meme_alph", "shuffle_string", "slide_fun", "utils-sequence", "window_string" ] }, { "page": "view_logo", "title": "Plot logos from numeric matrices.", "topics": [ "view_logo" ] }, { "page": "view_motifs", "title": "Plot motif logos.", "topics": [ "view_motifs" ] }, { "page": "view_motifs2", "title": "Plot motif logos using 'compare_motifs2()' alignment (v2).", "topics": [ "view_motifs2" ] }, { "page": "write_homer", "title": "Export motifs in HOMER format.", "concept": [ "write_motifs" ], "topics": [ "write_homer" ] }, { "page": "write_jaspar", "title": "Export motifs in JASPAR format.", "concept": [ "write_motifs" ], "topics": [ "write_jaspar" ] }, { "page": "write_matrix", "title": "Export motifs as raw matrices.", "concept": [ "write_motifs" ], "topics": [ "write_matrix" ] }, { "page": "write_meme", "title": "Export motifs in MEME format.", "concept": [ "write_motifs" ], "topics": [ "write_meme" ] }, { "page": "write_motifs", "title": "Export motifs in universalmotif format.", "concept": [ "write_motifs" ], "topics": [ "write_motifs" ] }, { "page": "write_transfac", "title": "Export motifs in TRANSFAC format.", "concept": [ "write_motifs" ], "topics": [ "write_transfac" ] } ], "_readme": "https://github.com/bioc/universalmotif/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "cli", "cpp11", "crayon", "farver", "generics", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lifecycle", "MASS", "MatrixGenerics", "matrixStats", "R6", "RColorBrewer", "Rcpp", "RcppThread", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "vctrs", "viridisLite", "withr", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "ChIPseqWorkflow.Rmd", "filename": "ChIPseqWorkflow.html", "title": "An end-to-end ChIP-seq workflow: from a peak BED to enriched motifs", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Loading peaks from a BED file", "Extracting peak sequences and building a matched background", "De novo motif discovery", "Deduplicating the discovered set", "Comparing against JASPAR via MotifDb", "Validating enrichment against a composition-matched background", "Scanning all peaks and testing positional bias", "Motif clustering with motif_coocc()", "Summary table", "Session info", "References" ], "created": "2026-05-25 10:59:28", "modified": "2026-05-30 07:22:08", "commits": 7 }, { "source": "MotifDatabaseCuration.Rmd", "filename": "MotifDatabaseCuration.html", "title": "Building a curated motif database from multiple sources", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Loading motifs from several sources", "Sidebar: importing raw files directly", "Inspecting cross-source redundancy", "Deduplicating via graph clustering", "Visualising the cluster structure", "Trimming uninformative flanks", "Adding the metadata back", "Export as a single MEME file", "Session info", "References" ], "created": "2026-05-26 09:22:51", "modified": "2026-05-30 07:22:08", "commits": 4 }, { "source": "Introduction.Rmd", "filename": "Introduction.html", "title": "Introduction to \"universalmotif\"", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Overview" ], "created": "2018-08-19 15:55:05", "modified": "2026-05-05 09:52:44", "commits": 9 }, { "source": "IntroductionToSequenceMotifs.Rmd", "filename": "IntroductionToSequenceMotifs.html", "title": "Introduction to sequence motifs", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Introduction to sequence motifs", "Position count matrices", "| Sequence", "Position probability matrices", "Position weight matrices", "Information content matrices", "References" ], "created": "2018-08-19 02:56:00", "modified": "2026-05-26 13:10:13", "commits": 24 }, { "source": "MotifComparisonAndPvalues.Rmd", "filename": "MotifComparisonAndPvalues.html", "title": "Motif comparisons and P-values", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Motif comparisons", "An overview of available comparison metrics", "Comparison parameters", "Comparison P-values", "A faster alternative: compare_motifs2()", "Speed comparison vs compare_motifs() and yamtk cmp", "Merging motifs", "A faster alternative: merge_motifs2() / merge_similar2()", "Motif trees with ggtree", "Using motif_tree()", "Using compare_motifs() and ggtree()", "Plotting motifs alongside trees", "Motif P-values", "The dynamic programming algorithm for calculating P-values and scores", "The branch-and-bound algorithm for calculating P-values from scores", "The random subsetting algorithm for calculating scores from P-values", "Session info", "References" ], "created": "2019-05-26 18:20:49", "modified": "2026-05-30 07:22:08", "commits": 36 }, { "source": "MotifManipulation.Rmd", "filename": "MotifManipulation.html", "title": "Motif import, export, and manipulation", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The universalmotif class and conversion utilities", "The universalmotif class", "Converting to and from another package's class", "Importing and exporting motifs", "Importing", "Exporting", "Modifying motifs and related functions", "Converting motif type", "Merging motifs", "Motif reverse complement", "Switching between DNA and RNA alphabets", "Motif trimming", "Rounding motifs", "Motif creation", "From a PCM/PPM/PWM/ICM matrix", "From sequences or character strings", "Generating random motifs", "Motif visualisation", "Motif logos", "Stacked motif logos", "Plot arbitrary text logos", "Higher-order motifs", "| Sequence", "Tidy motif manipulation with the universalmotif_df data structure", "Miscellaneous motif utilities", "DNA/RNA/AA consensus functions", "Filter through lists of motifs", "Generate random motif matches", "Motif shuffling", "Scoring and match functions", "Type conversion functions", "Session info", "References" ], "created": "2018-08-19 02:56:00", "modified": "2026-05-30 07:22:08", "commits": 39 }, { "source": "SequenceSearches.Rmd", "filename": "SequenceSearches.html", "title": "Sequence manipulation and scanning", "author": "Benjamin Jean-Marie Tremblay^[benjamin.tremblay@uwaterloo.ca]", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Basic sequence handling", "Creating random sequences", "Calculating sequence background", "Clustering sequences by k-let composition", "Shuffling", "Shuffling sequences", "Local shuffling", "Composition-matched backgrounds with match_bkg()", "Generating ground-truth positive sequences with implant_motifs()", "Motif pair co-occurrence with motif_coocc()", "Sequence scanning and enrichment", "Choosing a logodds threshold", "Logodds thresholds", "P-values", "Multiple testing-corrected P-values", "Regular and higher order scanning", "A faster alternative: scan_sequences2()", "Speed comparison vs motifmatchr and yamtk", "Visualizing motif hits across sequences", "Enrichment analyses", "A faster alternative: enrich_motifs2()", "De novo motif discovery", "Positional enrichment with motif_peaks()", "Fixed and variable-length gapped motifs", "Detecting low complexity regions and sequence masking", "Motif discovery with MEME", "Miscellaneous string utilities", "Session info", "References" ], "created": "2018-08-19 02:56:00", "modified": "2026-05-30 07:22:08", "commits": 67 } ], 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