{ "_id": "6a1ac1f61d7bb097a09d9245", "Package": "motifStack", "Type": "Package", "Version": "1.57.0", "Title": "Plot stacked logos for single or multiple DNA, RNA and amino\nacid sequence", "Authors@R": "c(person(given=\"Jianhong\", family=\"Ou\", email=\"jou@morgridge.org\", \nrole=c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-8652-2488\")),\nperson(given=\"Michael\", family=\"Brodsky\", role = \"ctb\",\nemail = \"Michael.Brodsky@umassmed.edu\"),\nperson(given=\"Scot\", family=\"Wolfe\", role = \"ctb\",\nemail = \"Scot.Wolfe@umassmed.edu\"),\nperson(\"Lihua Julie Zhu\", \"Developer\", role = \"aut\",\nemail = \"Julie.Zhu@umassmed.edu\"))", "Author": "Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu", "Maintainer": "Jianhong Ou ", "biocViews": "SequenceMatching, Visualization, Sequencing, Microarray,\nAlignment, ChIPchip, ChIPSeq, MotifAnnotation, DataImport", "Description": "The motifStack package is designed for graphic\nrepresentation of multiple motifs with different similarity\nscores. It works with both DNA/RNA sequence motif and amino\nacid sequence motif. In addition, it provides the flexibility\nfor users to customize the graphic parameters such as the font\ntype and symbol colors.", "License": "GPL (>= 2)", "Lazyload": "yes", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libgsl0-dev libbz2-dev liblzma-dev\nlibuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:36:53 UTC", "RemoteUrl": "https://github.com/bioc/motifStack", "RemoteRef": "HEAD", "RemoteSha": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:31:17 UTC", "User": "root" }, "MD5sum": "55cdf282376da4f42730ebf432dbad81", "_user": "bioc", "_type": "src", "_file": "motifStack_1.57.0.tar.gz", "_fileid": "ea1cb11f6a4355cf9fc5a7e183969eb96379c6fa0441c97b5f36ef953631618a", "_filesize": 1845633, "_sha256": "ea1cb11f6a4355cf9fc5a7e183969eb96379c6fa0441c97b5f36ef953631618a", "_created": "2026-05-30T07:31:17.000Z", "_published": "2026-05-30T10:54:46.190Z", "_jobs": [ { "job": 78633741012, "time": 232, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306519363" }, { "job": 78633741010, "time": 474, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306543840" }, { "job": 78633741015, "time": 445, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306541079" }, { "job": 78633741014, "time": 288, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307636568" }, { "job": 78633741011, "time": 242, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307632489" }, { "job": 78633386787, "time": 362, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306493418" }, { "job": 78633741008, "time": 181, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306513609" }, { "job": 78633741017, "time": 410, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306537748" }, { "job": 78633741021, "time": 357, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306532322" }, { "job": 78633741018, "time": 333, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306529962" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/motifStack", "_commit": { "id": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379813 }, "_maintainer": { "name": "Jianhong Ou", "email": "jou@morgridge.org", "orcid": "0000-0002-8652-2488" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.1", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "grid", "role": "Depends" }, { "package": "ade4", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "htmlwidgets", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stats4", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "XML", "role": "Imports" }, { "package": "TFBSTools", "role": "Imports" }, { "package": "Cairo", "role": "Suggests" }, { "package": "grImport", "role": "Suggests" }, { "package": "grImport2", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "MotifDb", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "JASPAR2020", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 6, "_updates": [ { "week": "2025-43", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.57.0", "bioc": "3.24" }, { "branch": "release", "version": "1.56.0", "bioc": "3.23" } ], "_topics": [ "sequencematching", "visualization", "sequencing", "microarray", "alignment", "chipchip", "chipseq", "motifannotation", "dataimport" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1575, "source": "https://www.bioconductor.org/packages/stats/bioc/motifStack" }, "_mentions": 10, "_searchresults": 281, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/motifStack.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jianhong/motifstack", "_realowner": "bioc", "_cranurl": false, "_exports": [ "AAmotifAlignment", "addBlank", "as.data.frame", "browseMotifs", "browseMotifsOutput", "clusterMotifs", "coerce", "colorset", "DNAmotifAlignment", "DNAmotifToRNAmotif", "format", "frequence", "geom_motif", "GeomMotif", "getIC", "getRankedUniqueMotifs", "highlightCol", "importMatrix", "matalign", "matrixReverseComplement", "mergeMotifs", "motifCircos", "motifCloud", "motifGrob", "motifHclust", "motifPiles", "motifSignature", "motifStack", "nodelist", "pcm2pfm", "pcm2pssm", "pfm2pwm", "plot", "plotAffinityLogo", "plotMotifLogo", "plotMotifLogoA", "plotMotifLogoStack", "plotMotifLogoStackWithTree", "plotMotifOverMotif", "plotMotifStackWithPhylog", "plotMotifStackWithRadialPhylog", "readPCM", "renderbrowseMotifs", "reorderUPGMAtree", "sigColor", "signatures", "trimMotif" ], "_help": [ { "page": "motifStack-package", "title": "Plot stacked logos for single or multiple DNA, RNA and amino acid sequence", "topics": [ "motifStack-package" ] }, { "page": "AAmotifAlignment", "title": "align AA motifs", "topics": [ "AAmotifAlignment" ] }, { "page": "browseMotifs", "title": "browse motifs", "topics": [ "browseMotifs" ] }, { "page": "browseMotifs-shiny", "title": "Shiny bindings for browseMotifs", "topics": [ "browseMotifs-shiny", "browseMotifsOutput", "renderbrowseMotifs" ] }, { "page": "calF", "title": "calculate frequence", "topics": [ "calF" ] }, { "page": "calI", "title": "calculate I'", "topics": [ "calI" ] }, { "page": "clusterMotifs", "title": "cluster motifs", "topics": [ "clusterMotifs" ] }, { "page": "colorset", "title": "retrieve color setting for logo", "topics": [ "colorset" ] }, { "page": "compare2profiles", "title": "compare two profiles", "topics": [ "compare2profiles" ] }, { "page": "compareProfiles", "title": "comapre w pcm", "topics": [ "compareProfiles" ] }, { "page": "DNAmotifAlignment", "title": "align DNA motifs", "topics": [ "DNAmotifAlignment" ] }, { "page": "DNAmotifToRNAmotif", "title": "convert DNA motif into RNA motif", "topics": [ "DNAmotifToRNAmotif" ] }, { "page": "dpGlobal", "title": "Global alignment version", "topics": [ "dpGlobal" ] }, { "page": "dpLocal", "title": "Dynamic programming function, local version", "topics": [ "dpLocal" ] }, { "page": "geom_motif", "title": "geom_motif", "topics": [ "geom_motif" ] }, { "page": "GeomMotif", "title": "GeomMotif object", "topics": [ "GeomMotif" ] }, { "page": "getALLRscoreFromCounts", "title": "calculate ALLR from counts", "topics": [ "getALLRscoreFromCounts" ] }, { "page": "getDistance", "title": "Calculate distances between two profiles", "topics": [ "getDistance" ] }, { "page": "getRankedUniqueMotifs", "title": "get the unique motif in each category grouped by distance", "topics": [ "getRankedUniqueMotifs" ] }, { "page": "getScore", "title": "Calculate pair_wise position score", "topics": [ "getScore" ] }, { "page": "highlightCol", "title": "add alpha transparency value to a color", "topics": [ "highlightCol" ] }, { "page": "importMatrix", "title": "import motifs from local files", "topics": [ "importMatrix" ] }, { "page": "marker-class", "title": "Class 'marker'", "topics": [ "$,marker-method", "$<-,marker-method", "marker", "marker-class" ] }, { "page": "matalign", "title": "Matrix Aligner", "topics": [ "matalign" ] }, { "page": "mergeMotifs", "title": "merge multiple motifs", "topics": [ "mergeMotifs" ] }, { "page": "motifCircos", "title": "plot sequence logo stacks with a radial phylogenic tree and multiple color rings", "topics": [ "motifCircos" ] }, { "page": "motifCloud", "title": "plot a DNA sequence logo cloud", "topics": [ "motifCloud" ] }, { "page": "motifGrob", "title": "Motif Grob", "topics": [ "motifGrob" ] }, { "page": "motifHclust", "title": "Hierarchical Clustering motifs", "topics": [ "motifHclust" ] }, { "page": "motifPiles", "title": "plot sequence logo stacks with a linear phylogenic tree and multiple color sets", "topics": [ "motifPiles" ] }, { "page": "motifSig-class", "title": "Class '\"motifSig\"'", "topics": [ "$,motifSig-method", "$<-,motifSig-method", "frequence", "frequence,motifSig-method", "motifSig", "motifSig-class", "nodelist", "nodelist,motifSig-method", "sigColor", "sigColor,motifSig-method", "signatures", "signatures,motifSig-method" ] }, { "page": "motifSignature", "title": "get signatures from motifs", "topics": [ "motifSignature" ] }, { "page": "motifStack", "title": "plot a DNA sequence logo stack", "topics": [ "motifStack" ] }, { "page": "ouNode-class", "title": "Class 'ouNode'", "topics": [ "$,ouNode-method", "$<-,ouNode-method", "ouNode", "ouNode-class" ] }, { "page": "pcm-class", "title": "Class '\"pcm\"'", "topics": [ "$,pcm-method", "$<-,pcm-method", "addBlank", "addBlank,pcm,numeric,logical-method", "as", "as.data.frame,pcm-method", "coerce,pcm,matrix-method", "format,pcm-method", "getIC", "getIC,pcm,ANY-method", "matrixReverseComplement", "matrixReverseComplement,pcm-method", "pcm", "pcm-class", "pcm2pfm", "pcm2pfm,data.frame,ANY-method", "pcm2pfm,data.frame,numeric-method", "pcm2pfm,list,ANY-method", "pcm2pfm,list,numeric-method", "pcm2pfm,matrix,ANY-method", "pcm2pfm,matrix,numeric-method", "pcm2pfm,pcm,ANY-method", "pcm2pssm", "pcm2pssm,data.frame,ANY-method", "pcm2pssm,data.frame,numeric-method", "pcm2pssm,list,ANY-method", "pcm2pssm,list,numeric-method", "pcm2pssm,matrix,ANY-method", "pcm2pssm,matrix,numeric-method", "pcm2pssm,pcm,ANY-method", "plot", "plot,pcm,ANY-method", "trimMotif", "trimMotif,pcm,numeric-method" ] }, { "page": "pfm-class", "title": "Class '\"pfm\"'", "topics": [ "$,pfm-method", "$<-,pfm-method", "addBlank,pfm,numeric,logical-method", "as.data.frame,pfm-method", "coerce", "coerce,pfm,matrix-method", "format,pfm-method", "getIC,matrix,matrix-method", "getIC,matrix,numeric-method", "getIC,pfm,ANY-method", "matrixReverseComplement,pfm-method", "pfm", "pfm-class", "plot,pfm,ANY-method", "trimMotif,pfm,numeric-method" ] }, { "page": "pfm2pwm", "title": "convert pfm object to PWM", "topics": [ "pfm2pwm" ] }, { "page": "plotAffinityLogo", "title": "plot affinity logo", "topics": [ "plotAffinityLogo" ] }, { "page": "plotMotifLogo", "title": "plot sequence logo", "topics": [ "plotMotifLogo" ] }, { "page": "plotMotifLogoA", "title": "plot sequence logo without plot.new", "topics": [ "plotMotifLogoA" ] }, { "page": "plotMotifLogoStack", "title": "plot sequence logos stack", "topics": [ "plotMotifLogoStack" ] }, { "page": "plotMotifLogoStackWithTree", "title": "plot sequence logos stack with hierarchical cluster tree", "topics": [ "plotMotifLogoStackWithTree" ] }, { "page": "plotMotifOverMotif", "title": "plot motif over another motif", "topics": [ "plotMotifOverMotif" ] }, { "page": "plotMotifStackWithPhylog", "title": "plot sequence logo stacks with a ape4-style phylogenic tree", "topics": [ "plotMotifStackWithPhylog" ] }, { "page": "plotMotifStackWithRadialPhylog", "title": "plot sequence logo stacks with a radial phylogenic tree", "topics": [ "plotMotifStackWithRadialPhylog" ] }, { "page": "plotXaxis", "title": "plot x-axis", "topics": [ "plotXaxis" ] }, { "page": "plotYaxis", "title": "plot y-axis", "topics": [ "plotYaxis" ] }, { "page": "psam-class", "title": "Class '\"psam\"'", "topics": [ "$,psam-method", "$<-,psam-method", "addBlank,psam,numeric,logical-method", "as()", "as.data.frame,psam-method", "coerce,psam,matrix-method", "format,psam-method", "matrixReverseComplement,psam-method", "plot,psam,ANY-method", "psam", "psam-class" ] }, { "page": "pssm-class", "title": "Class '\"pssm\"'", "topics": [ "$,pssm-method", "$<-,pssm-method", "addBlank,pssm,numeric,logical-method", "as.data.frame,pssm-method", "coerce()", "coerce,pssm,matrix-method", "format,pssm-method", "matrixReverseComplement,pssm-method", "plot,pssm,ANY-method", "pssm", "pssm-class" ] }, { "page": "readPCM", "title": "read pcm from a path", "topics": [ "readPCM" ] }, { "page": "reorderUPGMAtree", "title": "re-order UPGMA tree", "topics": [ "reorderUPGMAtree" ] }, { "page": "traceBackGlobal", "title": "traceback global", "topics": [ "traceBackGlobal" ] }, { "page": "traceBackLocal", "title": "traceback local", "topics": [ "traceBackLocal" ] } ], "_readme": "https://github.com/bioc/motifStack/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "caTools", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "digest", "DirichletMultinomial", "evaluate", "farver", "fastmap", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "gtools", "highr", "htmltools", "htmlwidgets", "httr", "IRanges", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pixmap", "pkgconfig", "pwalign", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "seqLogo", "snow", "sp", "SparseArray", "SummarizedExperiment", "sys", "TFBSTools", "TFMPvalue", "tinytex", "vctrs", "viridisLite", "withr", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "motifStack_HTML.Rmd", "filename": "motifStack_HTML.html", "title": "motifStack Vignette", "author": "Jianhong Ou, Michael Brodsky, Lihua Julie Zhu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Import matrix", "convert motifs from XMatrixList", "import motifs from files", "Examples of using motifStack", "plot a DNA sequence logo with different fonts and colors", "plot sequence logo with markers", "change the x-axis labels", "plot a RNA sequence logo", "plot an amino acid sequence logo", "plot an affinity logo", "plot sequence logo stack", "plot a sequence logo cloud", "plot grouped sequence logo", "motifCircos", "motifPiles", "plot motifs with d3.js", "docker container for motifStack", "plot motifs with ggplot2", "Session Info", "Reference" ], "created": "2015-09-29 15:07:37", "modified": "2022-04-19 12:23:16", "commits": 35 } ], "_score": 8.077350642189687, "_indexed": true, "_nocasepkg": "motifstack", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.57.0", "date": "2026-05-30T07:35:46.000Z", "distro": "noble", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "bd3abddadab574fe90fa1e3d2dbe4de2aead7a6bbc7f8eb62a14b17b2a762b5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.6.0", "os": "linux", "version": "1.57.0", "date": "2026-05-30T07:35:37.000Z", "distro": "noble", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "1f21fd3241622144670a0b5cf87712e467b1cab2a3798a48d8c8827fe044e21f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.5.3", "os": "mac", "version": "1.57.0", "date": "2026-05-30T10:46:39.000Z", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "85fe58b2d5523826b75ea1da029def930b0c0749d817ee71bde38786ba684e56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.6.0", "os": "mac", "version": "1.57.0", "date": "2026-05-30T10:46:35.000Z", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "5594b27667027bb580dca3cf174919160cf3fda6ff99c1d3bc8a8c3a88101dc8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.6.0", "os": "wasm", "version": "1.57.0", "date": "2026-05-30T07:35:05.000Z", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "cee8724c03cdc63d1bbe76f89259ee3e96c0d039ed7fdd2836b7e5d6db9474d2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.7.0", "os": "win", "version": "1.57.0", "date": "2026-05-30T07:33:37.000Z", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "c488d6c7893f02ccad9b4267055ff3021ba72b54bf5d2f4dc88dde2b9b3eba6d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.5.3", "os": "win", "version": "1.57.0", "date": "2026-05-30T07:33:46.000Z", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "2e54d7fd2be315c2234cdb0424f7416b13a905a29ad25eb511635b898432f46e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" }, { "r": "4.6.0", "os": "win", "version": "1.57.0", "date": "2026-05-30T07:33:30.000Z", "commit": "3f6e3dc6940b9aa8b2866e4cf49371feb2a611a8", "fileid": "e26e82ea417ac9a643fc1657188cdebc4810f62da60921fbb9846fcb08050885", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678026814" } ] }