{ "_id": "6ab46b4c3d719c1f84094ecc", "Type": "Package", "Package": "TSSr", "Title": "TSS sequencing data analysis", "Version": "0.99.21", "Date": "2026-08-21", "Authors@R": "c(\nperson(\"Zhaolian\", \"Lu\", , \"luzhaolian@gmail.com\", role = c(\"aut\", \"com\"),\ncomment = c(ORCID = \"0000-0001-5002-7007\")),\nperson(\"Keenan\", \"Berry\", , \"keenan.berry@slu.edu\", role = c(\"aut\", \"com\")),\nperson(\"Zhenbin\", \"Hu\", , \"zhenbin.hu@slu.edu\", role = c(\"aut\", \"ctb\")),\nperson(\"Yu\", \"Zhan\", , \"yu.zhan@slu.edu\", role = c(\"aut\", \"ctb\")),\nperson(\"Tae-Hyuk (Ted)\", \"Ahn\", , \"ted.ahn@slu.edu\", role = c(\"aut\", \"cph\")),\nperson(\"Zhenguo\", \"Lin\", , \"zhenguo.lin@slu.edu\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-8400-9138\")),\nperson(\"National Science Foundation\", role = \"fnd\",\ncomment = \"NSF 1951332\")\n)", "Description": "TSSr package provides a comprehensive workflow on TSS data\nstarts from identification of accurate TSS locations,\nclustering TSSs within small genomic regions corresponding to\ncore promoters, and transcriptional activity quantifications,\nas well as specialized downstream analyses including core\npromoter shape, cluster annotation, gene differential\nexpression, core promoter shift. TSSr can take multiple formats\nof files as input, such as Binary Sequence Alignment Map (BAM)\nfiles (single-ended or paired-ended), Browser Extension Data\n(bed) files, BigWig files, ctss files or tss tables. TSSr also\ngenerates various types of TSS or core promoter track files\nwhich can be visualized in the UCSC Genome Browser or\nIntegrative Genomics Viewer (IGV). TSSr also exports downstream\nanalyses result tables and plots. Multiple cores are supported\non Linux or Mac platforms.", "License": "MIT + file LICENSE", "URL": "https://github.com/Linlab-slu/TSSr", "BugReports": "https://github.com/Linlab-slu/TSSr/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "FALSE", "NeedsCompilation": "no", "RoxygenNote": "7.3.3", "biocViews": "Software, Transcription, Coverage, GeneExpression,\nGeneRegulation, PeakDetection, DataImport, DataRepresentation,\nTranscriptomics, Sequencing, Annotation, GenomeBrowsers,\nNormalization, Preprocessing, Visualization,\nDifferentialExpression, Alignment, Clustering", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-21 20:41:36 UTC", "RemoteUrl": "https://github.com/bioc/TSSr", "RemoteRef": "HEAD", "RemoteSha": "bba29ddb31aa3bcc5c8e1a4276224de759b5b7ea", "Packaged": { "Date": "2026-09-24 00:03:01 UTC", "User": "root" }, "Author": "Zhaolian Lu [aut, com] (ORCID: ),\nKeenan Berry [aut, com],\nZhenbin Hu [aut, ctb],\nYu Zhan [aut, ctb],\nTae-Hyuk (Ted) Ahn [aut, cph],\nZhenguo Lin [aut, cre, cph] (ORCID:\n),\nNational Science Foundation [fnd] (NSF 1951332)", "Maintainer": "Zhenguo Lin ", "_user": "bioc", "_type": "src", "_file": "TSSr_0.99.21.tar.gz", "_fileid": "https://r2.ropensci.org/c5c414cabb3b79dc8734edaeea951fb10d25d61cdbbcfe5533fb0c8b439ca80f", "_filesize": 1031080, "_sha256": "c5c414cabb3b79dc8734edaeea951fb10d25d61cdbbcfe5533fb0c8b439ca80f", "_expires": "2027-01-02T00:14:02.000Z", "_created": "2026-09-24T00:03:01.000Z", "_published": "2026-09-24T00:14:04.403Z", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35936124586", "_status": "success", "_upstream": "https://github.com/bioc/TSSr", "_commit": { "id": "bba29ddb31aa3bcc5c8e1a4276224de759b5b7ea", "author": 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"title": "Make consensus clusters across multiple samples.", "topics": [ "consensusCluster", "consensusCluster,TSSr-method" ] }, { "page": "deGene", "title": "Analysis of gene differential expression.", "topics": [ "deGene", "deGene,TSSr-method" ] }, { "page": "exampleTSSr", "title": "TSSr example data", "topics": [ "exampleTSSr" ] }, { "page": "exportClustersTable", "title": "Export cluster tables", "topics": [ "exportClustersTable", "exportClustersTable,TSSr-method" ] }, { "page": "exportClustersToBed", "title": "Creating bed files of clusters", "topics": [ "exportClustersToBed", "exportClustersToBed,TSSr-method" ] }, { "page": "exportDETable", "title": "Export gene differential expression results table", "topics": [ "exportDETable", "exportDETable,TSSr-method" ] }, { "page": "exportEnhancerTable", "title": "Export enhancer tables", "topics": [ "exportEnhancerTable", "exportEnhancerTable,TSSr-method" ] }, { "page": "exportShapeTable", "title": "Export core promoter shape score tables", "topics": [ "exportShapeTable", "exportShapeTable,TSSr-method" ] }, { "page": "exportShiftTable", "title": "Export core promoter shift table", "topics": [ "exportShiftTable", "exportShiftTable,TSSr-method" ] }, { "page": "exportTSStable", "title": "Export TSS tables", "topics": [ "exportTSStable", "exportTSStable,TSSr-method" ] }, { "page": "exportTSStoBedgraph", "title": "Creating Bedgraph/BigWig tracks of TSSs", "topics": [ "exportTSStoBedgraph", "exportTSStoBedgraph,TSSr-method" ] }, { "page": "filterTSS", "title": "Filter raw TSS counts or normalized TSS", "topics": [ "filterTSS", "filterTSS,TSSr-method" ] }, { "page": "getTSS", "title": "Precisely identify TSSs from bam files, paired end bam files, bed files, BigWig files, tss files, or tss tables.", "topics": [ "getTSS", "getTSS,TSSr-method" ] }, { "page": "mergeSamples", "title": "Merge TSS samples", "topics": [ "mergeSamples", "mergeSamples,TSSr-method" ] }, { "page": "normalizeTSS", "title": "Normalize raw TSS counts", "topics": [ "normalizeTSS", "normalizeTSS,TSSr-method" ] }, { "page": "plotCorrelation", "title": "Pairwise scatter plots and correlations of TSS signal", "topics": [ "plotCorrelation", "plotCorrelation,TSSr-method" ] }, { "page": "plotDE", "title": "Plot gene differential expressions", "topics": [ "plotDE", "plotDE,TSSr-method" ] }, { "page": "plotInterQuantile", "title": "Plot core promoter interquantile width", "topics": [ "plotInterQuantile", "plotInterQuantile,TSSr-method" ] }, { "page": "plotShape", "title": "Plot core promoter shape", "topics": [ "plotShape", "plotShape,TSSr-method" ] }, { "page": "plotTSS", "title": "Plot TSSs and clusters", "topics": [ "plotTSS", "plotTSS,TSSr-method" ] }, { "page": "plotTssPCA", "title": "Plotting principle component analysis (PCA)", "topics": [ "plotTssPCA", "plotTssPCA,TSSr-method" ] }, { "page": "shapeCluster", "title": "Analysis of core promoter shape", "topics": [ "shapeCluster", "shapeCluster,TSSr-method" ] }, { "page": 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