{ "_id": "6a1acbfc1d7bb097a09de402", "Package": "icetea", "Type": "Package", "Title": "Integrating Cap Enrichment with Transcript Expression Analysis", "Version": "1.31.0", "Authors@R": "person(\"Vivek\", \"Bhardwaj\", email = \"v.bhardwaj@hubrecht.eu\", role = c(\"aut\", \"cre\"))", "Description": "icetea (Integrating Cap Enrichment with Transcript\nExpression Analysis) provides functions for end-to-end analysis\nof multiple 5'-profiling methods such as CAGE, RAMPAGE and\nMAPCap, beginning from raw reads to detection of transcription\nstart sites using replicates. It also allows performing\ndifferential TSS detection between group of samples, therefore,\nintegrating the mRNA cap enrichment information with transcript\nexpression analysis.", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, Transcription, GeneExpression, Sequencing,\nRNASeq, Transcriptomics, DifferentialExpression", "URL": "https://github.com/vivekbhr/icetea", "BugReports": "https://github.com/vivekbhr/icetea/issues", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "make libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:11 UTC", "RemoteUrl": "https://github.com/bioc/icetea", "RemoteRef": "HEAD", "RemoteSha": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:00:59 UTC", "User": "root" }, "Author": "Vivek Bhardwaj [aut, cre]", "Maintainer": "Vivek Bhardwaj ", "MD5sum": "2cc4edf6c4e981c0658ad1fee173b552", "_user": "bioc", "_type": "src", "_file": "icetea_1.31.0.tar.gz", "_fileid": "8b2f90e43684abab5f2876789ee445cb415bb1abae52e678f59addd840dc56f8", "_filesize": 777769, "_sha256": "8b2f90e43684abab5f2876789ee445cb415bb1abae52e678f59addd840dc56f8", "_created": "2026-05-30T08:00:59.000Z", "_published": "2026-05-30T11:37:32.422Z", "_jobs": [ { "job": 78635238423, "time": 249, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306697377" }, { "job": 78635238420, "time": 574, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306730037" }, { "job": 78635238447, "time": 525, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306724998" }, { "job": 78635238446, "time": 278, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307894701" }, { "job": 78635238430, "time": 280, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307894065" }, { "job": 78634906763, "time": 370, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306673467" }, { "job": 78635238414, "time": 201, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306692793" }, { "job": 78635238435, "time": 559, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306728353" }, { "job": 78635238437, "time": 456, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306717753" }, { "job": 78635238433, "time": 519, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306724458" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/icetea", "_commit": { "id": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380491 }, "_maintainer": { "name": "Vivek Bhardwaj", "email": "v.bhardwaj@hubrecht.eu", "login": "vivekbhr", "twitter": "@vivekbhr", "description": "Researcher in Computational and Quantitative Genomics ", "uuid": 8420267 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "ShortRead", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "csaw", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "TxDb.Dmelanogaster.UCSC.dm6.ensGene", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Rsubread", "version": ">= 1.29.0", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "transcription", "geneexpression", "sequencing", "rnaseq", "transcriptomics", "differentialexpression", "cage", "expression", "rna-seq" ], "_stars": 2, "_contributors": [ { "user": "vivekbhr", "count": 33, "uuid": 8420267 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 364, "source": "https://www.bioconductor.org/packages/stats/bioc/icetea" }, "_mentions": 2, "_devurl": "https://github.com/vivekbhr/icetea", "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/icetea.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/vivekbhr/icetea", "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotateTSS", "demultiplexFASTQ", "detectDiffTSS", "detectTSS", "exampleCSobject", "exportTSS", "filterDuplicates", "fitDiffTSS", "getGeneCounts", "getNormFactors", "mapCaps", "newCapSet", "plotReadStats", "plotTSSprecision", "sampleInfo", "sampleInfo<-", "splitBAM_byIndex", "splitBAM_byRepindex" ], "_help": [ { "page": "activeChrs", "title": "Match BAM headers bw files and get active chromosome list (from restrict) (written by Aaron Lun, 12 Dec 2014, copied and modified here)", "topics": [ "activeChrs" ] }, { "page": "annotateTSS", "title": "Annotate the provided Transcription Start Sites", "topics": [ "annotateTSS" ] }, { "page": "check_capSet", "title": "Check capset validity", "topics": [ "check_capSet" ] }, { "page": "demultiplexFASTQ", "title": "Demultiplex and tag fastq files using sample barcodes", "topics": [ "demultiplexFASTQ", "demultiplexFASTQ,CapSet-method" ] }, { "page": "detectDiffTSS", "title": "Detect differentially expressed Transcription Start Sites between two conditions (test)", "topics": [ "detectDiffTSS", "detectDiffTSS,DESeqDataSet-method", "detectDiffTSS,DGEGLM-method" ] }, { "page": "detectTSS", "title": "Detection of Trancription start sites based on local enrichment", "topics": [ "detectTSS", "detectTSS,CapSet-method" ] }, { "page": "diffQCplots", "title": "Make DESeq2 or edgeR QC plots", "topics": [ "diffQCplots" ] }, { "page": "exampleCSobject", "title": "Create example CapSet object", "topics": [ "exampleCSobject" ] }, { "page": "exportTSS", "title": "Export the detected TSS from CapSet object as .bed files", "topics": [ "exportTSS", "exportTSS,CapSet-method" ] }, { "page": "filterDuplicates", "title": "Filter PCR-duplicates from mapped files using internal UMIs", "topics": [ "filterDuplicates", "filterDuplicates,CapSet-method" ] }, { "page": "filterDups", "title": "Filter PCR-duplicates from BAM file using internal UMIs", "topics": [ "filterDups" ] }, { "page": "fitDiffTSS", "title": "Detect differentially expressed Transcription Start Sites between two conditions (fit model)", "topics": [ "fitDiffTSS", "fitDiffTSS,CapSet-method" ] }, { "page": "get_newfastq", "title": "Get data to create new ShortReadQ object after barcode trimming", "topics": [ "get_newfastq" ] }, { "page": "getBamFlags", "title": "Get flags to read from bam", "topics": [ "getBamFlags" ] }, { "page": "getChromBins", "title": "Get chromosome bins from BAM files", "topics": [ "getChromBins" ] }, { "page": "getChromWindows", "title": "Get chromosome sliding windows from BAM files", "topics": [ "getChromWindows" ] }, { "page": "getGeneCounts", "title": "Get gene-level counts from TSS data", "topics": [ "getGeneCounts", "getGeneCounts,CapSet-method" ] }, { "page": "getMCparams", "title": "Get platform-specific multicore params", "topics": [ "getMCparams" ] }, { "page": "getNormFactors", "title": "Calculate normalization factors from CapSet object", "topics": [ "getNormFactors", "getNormFactors,CapSet-method" ] }, { "page": "getranks", "title": "Assign feature ranks on a VariantAnnotation output", "topics": [ "getranks" ] }, { "page": "mapCaps", "title": "Map the data from 5' profiling techniques", "topics": [ "mapCaps", "mapCaps,CapSet-method" ] }, { "page": "newCapSet", "title": "Create a new CapSet object", "topics": [ "CapSet", "CapSet-class", "newCapSet" ] }, { "page": "numReadsInBed", "title": "Count the number of reads in a given GRanges", "topics": [ "numReadsInBed" ] }, { "page": "plotPrecision", "title": "Plotprecision background script", "topics": [ "plotPrecision" ] }, { "page": "plotReadStats", "title": "Plot read statistics from the CapSet object", "topics": [ "plotReadStats", "plotReadStats,CapSet-method" ] }, { "page": "plotTSSprecision", "title": "Compare the precision of TSS detection between multiple samples", "topics": [ "plotTSSprecision", "plotTSSprecision,GRanges,CapSet-method", "plotTSSprecision,GRanges,character-method" ] }, { "page": "readsTo3p", "title": "preprocess reads to count only 3' overlaps", "topics": [ "readsTo3p" ] }, { "page": "readsTo5p", "title": "preprocess reads to count only 5' overlaps", "topics": [ "readsTo5p" ] }, { "page": "readsToCenter", "title": "preprocess reads to count only center overlaps", "topics": [ "readsToCenter" ] }, { "page": "sampleInfo", "title": "Retrieve and replace sample information of a CapSet object", "topics": [ "sampleInfo", "sampleInfo,CapSet-method", "sampleInfo<-", "sampleInfo<-,CapSet-method" ] }, { "page": "split_fastq", "title": "Split paired-end fastq by barcodes", "topics": [ "split_fastq" ] }, { "page": "splitBAM_byIndex", "title": "Split the composite BAM file using internal indexes (MAPCap)", "topics": [ "splitBAM_byIndex" ] }, { "page": "splitBAM_byRepindex", "title": "Split the composite BAM file using replicate indexes (MAPCap data)", "topics": [ "splitBAM_byRepindex" ] }, { "page": "splitranks", "title": "Get features with the best rank for each TSS", "topics": [ "splitranks" ] }, { "page": "strandBinCounts", "title": "Perform stranded Bin counts", "topics": [ "strandBinCounts" ] } ], "_readme": "https://github.com/bioc/icetea/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "csaw", "curl", "DBI", "DelayedArray", "deldir", "DESeq2", "edgeR", "farver", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gtable", "httr", "hwriter", "interp", "IRanges", "isoband", "jpeg", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "latticeExtra", "lifecycle", "limma", "locfit", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "metapod", "mime", "openssl", "pkgconfig", "png", "pwalign", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "ShortRead", "snow", "SparseArray", "statmod", "SummarizedExperiment", "sys", "TxDb.Dmelanogaster.UCSC.dm6.ensGene", "VariantAnnotation", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "mapcap_analysis.Rmd", "filename": "mapcap_analysis.html", "title": "Analysing transcript 5'-profiling data using icetea", "author": "Vivek Bhardwaj and Thomas Manke", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quick Start", "Help and citations", "How to get help", "How to cite ICETEA", "The CapSet object", "Analysis workflow", "De-multiplexing the fastq", "Mapping the fastqs", "(optional) Post mapping de-multiplexing", "Filtering PCR duplicates", "Detection of TSS", "Plotting and QC", "Differential TSS expression analysis", "Using spike-In controls", "Additional useful functions", "Getting the gene counts", "Annotating the TSS distribution", "References" ], "created": "2018-02-19 12:24:17", "modified": "2025-07-23 23:14:12", "commits": 10 } ], "_score": 5.369215857410143, "_indexed": true, "_nocasepkg": "icetea", "_universes": [ "bioc", "vivekbhr" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-05-30T08:06:10.000Z", "distro": "noble", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "0acfbc8e093cea55ad9f2f34e5f219c63e468d3a32743f02266f6c093fbc2231", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.6.0", "os": "linux", "version": "1.31.0", "date": "2026-05-30T08:05:47.000Z", "distro": "noble", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "d66f38fbc84230a13ca0958a21e0c3d567cd6654ea58f394e1680daf5b065031", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-05-30T11:34:09.000Z", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "5cf727c7856f2941dbb03249d952b30821deed4fced28f610cea527cec6fb31e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.6.0", "os": "mac", "version": "1.31.0", "date": "2026-05-30T11:33:55.000Z", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "168a9317f04b6b988e42f63cad71e6a8ecd3c2ebcc24e7c7dad29ab179c7e933", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-05-30T08:05:09.000Z", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "0ced4a60959ae4269d726b993e3d1003e01eb6a87658602f849faff0c8dc8a6c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-05-30T08:04:16.000Z", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "ed8bdf5a005578ee770c682cc226fe2fbb9adbec55ff52505a05f4bb4b51dabe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-05-30T08:03:41.000Z", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "abc334edf394f011440b931e49b3612a58000dcb68b12e653657e77740aef296", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" }, { "r": "4.6.0", "os": "win", "version": "1.31.0", "date": "2026-05-30T08:04:16.000Z", "commit": "0b56cf444247b10a5e248703d9d6fd6618d3ff89", "fileid": "f92d887b12ac7ffcafea59c1d8aa6b3b501a507587480eb87b83d2fa68c86db9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678601980" } ] }