{ "_id": "6a196862acfb0bcc41de8763", "Package": "CellBarcode", "Type": "Package", "Title": "Cellular DNA Barcode Analysis toolkit", "Version": "1.18.0", "Authors@R": "c(\nperson(\"Wenjie\", \"Sun\", email = \"sunwjie@gmail.com\", role = c(\"cre\", \"aut\"), comment=c(ORCID=\"0000-0002-3100-2346\")),\nperson(\"Anne-Marie\", \"Lyne\", email = \"Anne-Marie.Lyne@curie.fr\", role = \"aut\"),\nperson(\"Leila\", \"Perie\", email = \"leila.perie@curie.fr\", role = \"aut\")\n)", "Description": "The package CellBarcode performs Cellular DNA Barcode\nanalysis. It can handle all kinds of DNA barcodes, as long as\nthe barcode is within a single sequencing read and has a\npattern that can be matched by a regular expression.\n\\code{CellBarcode} can handle barcodes with flexible lengths,\nwith or without UMI (unique molecular identifier). This tool\nalso can be used for pre-processing some amplicon data such as\nCRISPR gRNA screening, immune repertoire sequencing, and\nmetagenome data.", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "biocViews": "Preprocessing, QualityControl, Sequencing, CRISPR", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "URL": "https://wenjie1991.github.io/CellBarcode/", "BugReports": "https://github.com/wenjie1991/CellBarcode/issues", "Config/pak/sysreqs": "libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:57:27 UTC", "RemoteUrl": "https://github.com/bioc/CellBarcode", "RemoteRef": "RELEASE_3_23", "RemoteSha": "18ef734c362c53e3bc4ff8c2cd883e18f207914e", "Packaged": { "Date": "2026-05-29 08:15:14 UTC", "User": "root" }, "Author": "Wenjie Sun [cre, aut] (ORCID: ),\nAnne-Marie Lyne [aut],\nLeila Perie [aut]", 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"bc_seq_qc", "bc_splitVDJ", "bc_subset", "bc_summary_barcode", "bc_summary_seqQc", "format", "show" ], "_datasets": [ { "name": "bc_obj", "title": "A dummy BarcodeObj object", "object": "bc_obj", "file": "bc_obj.RData", "class": [ "BarcodeObj" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "BarcodeObj", "title": "BarcodeObj object", "topics": [ "BarcodeObj", "BarcodeObj-class" ] }, { "page": "bc_2df", "title": "Transforms BarcodeObj object into another data type", "topics": [ "bc_2df", "bc_2df,BarcodeObj-method", "bc_2dt", "bc_2dt,BarcodeObj-method", "bc_2matrix", "bc_2matrix,BarcodeObj-method" ] }, { "page": "bc_auto_cutoff", "title": "Finds barcode count cutoff point", "topics": [ "bc_auto_cutoff", "bc_auto_cutoff,BarcodeObj-method" ] }, { "page": "bc_barcodes", "title": "Gets barcode sequences", "topics": [ "bc_barcodes", "bc_barcodes,BarcodeObj-method" ] }, { "page": "bc_cleanBc", "title": "Accesses cleanBc slot in the BarcodeObj object", "topics": [ "bc_cleanBc", "bc_cleanBc,BarcodeObj-method" ] }, { "page": "bc_create_BarcodeObj", "title": "Create a BarcodeObj object from extracted barcodes data", "topics": [ "bc_create_BarcodeObj", "bc_create_BarcodeObj,data.frame-method", "bc_create_BarcodeObj,matrix-method" ] }, { "page": "bc_cure_cluster", "title": "Clean barcodes by editing distance", "topics": [ "bc_cure_cluster", "bc_cure_cluster,BarcodeObj-method" ] }, { "page": "bc_cure_depth", "title": "Filters barcodes by counts", "topics": [ "bc_cure_depth", "bc_cure_depth,BarcodeObj-method" ] }, { "page": "bc_cure_umi", "title": "Filters UMI-barcode tag by counts", "topics": [ "bc_cure_umi", "bc_cure_umi,BarcodeObj-method" ] }, { "page": "bc_extract", "title": "Extract barcode from sequences", "topics": [ "bc_extract", "bc_extract,character-method", "bc_extract,data.frame-method", "bc_extract,DNAStringSet-method", "bc_extract,integer-method", "bc_extract,list-method", "bc_extract,ShortReadQ-method" ] }, { "page": "bc_extract_sc_fastq", "title": "Extract barcode from single-cell sequencing fastq file", "topics": [ "bc_extract_sc_fastq" ] }, { "page": "bc_extract_sc_sam", "title": "Extract barcode from single-cell sequencing sam file", "topics": [ "bc_extract_sc_bam", "bc_extract_sc_sam" ] }, { "page": "bc_messyBc", "title": "Accesses messyBc slot in the BarcodeObj object", "topics": [ "bc_messyBc", "bc_messyBc,BarcodeObj-method" ] }, { "page": "bc_meta", "title": "Accesses and sets metadata in BarcodeObj object", "topics": [ "bc_meta", "bc_meta,BarcodeObj-method", "bc_meta<-", "bc_meta<-,BarcodeObj-method" ] }, { "page": "bc_names", "title": "Access & update sample names in BarcodeObj & and BarcodeQcSet", "topics": [ "bc_names", "bc_names,BarcodeObj-method", "bc_names,BarcodeQcSet-method", "bc_names<-", "bc_names<-,BarcodeObj,character-method", "bc_names<-,BarcodeQcSet,ANY-method" ] }, { "page": "bc_obj", "title": "A dummy BarcodeObj object", "topics": [ "bc_obj" ] }, { "page": "bc_plot_count", "title": "Plot for counts distribution", "topics": [ "bc_plot_count", "bc_plot_count,BarcodeObj-method" ] }, { "page": "bc_plot_mutual", "title": "Barcode read count 2D scatter plot of sample combination", "topics": [ "bc_plot_mutual", "bc_plot_mutual,BarcodeObj-method" ] }, { "page": "bc_plot_pair", "title": "Barcode read count 2D scatter plot for given pairs", "topics": [ "bc_plot_pair", "bc_plot_pair,BarcodeObj-method" ] }, { "page": "bc_plot_single", "title": "Scatter plot of barcode count distribution per sample", "topics": [ "bc_plot_single", "bc_plot_single,BarcodeObj-method" ] }, { "page": "bc_seq_filter", "title": "Remove low-quality sequence", "topics": [ "bc_seq_filter", "bc_seq_filter,character-method", "bc_seq_filter,data.frame-method", "bc_seq_filter,DNAStringSet-method", "bc_seq_filter,integer-method", "bc_seq_filter,list-method", "bc_seq_filter,ShortReadQ-method" ] }, { "page": "bc_seq_qc", "title": "Evaluates sequences quality", "topics": [ "BarcodeQc", 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