{ "_id": "6a1aeee21d7bb097a09f5bc3", "Package": "scPipe", "Title": "Pipeline for single cell multi-omic data pre-processing", "Date": "2022-10-12", "Version": "2.12.0", "Type": "Package", "Authors@R": "c(person(\"Luyi\", \"Tian\", role=c(\"aut\"), email=\"tian.l@wehi.edu.au\"), \nperson(\"Shian\", \"Su\", role=c(\"aut\", \"cre\"), email=\"su.s@wehi.edu.au\"),\nperson(\"Shalin\", \"Naik\", role=c(\"ctb\"), email=\"naik.s@wehi.edu.au\"),\nperson(\"Shani\", \"Amarasinghe\", role=c(\"aut\"), email=\"amarasinghe.s@wehi.edu.au\"),\nperson(\"Oliver\", \"Voogd\", role=c(\"aut\"), email=\"voogd.o@wehi.edu.au\"),\nperson(\"Phil\", \"Yang\", role=c(\"aut\"), email=\"yang.p@wehi.edu.au\"),\nperson(\"Matthew\", \"Ritchie\", role=c(\"ctb\"), email=\"mritchie@wehi.edu.au\"))", "biocViews": "ImmunoOncology, Software, Sequencing, RNASeq,\nGeneExpression, SingleCell, Visualization, SequenceMatching,\nPreprocessing, QualityControl, GenomeAnnotation, DataImport", "Description": "A preprocessing pipeline for single cell RNA-seq/ATAC-seq\ndata that starts from the fastq files and produces a feature\ncount matrix with associated quality control information. It\ncan process fastq data generated by CEL-seq, MARS-seq,\nDrop-seq, Chromium 10x and SMART-seq protocols.", "SystemRequirements": "C++11, GNU make", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "yes", "URL": "https://github.com/LuyiTian/scPipe", "BugReports": "https://github.com/LuyiTian/scPipe", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev python3 xz-utils\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:46:40 UTC", "RemoteUrl": "https://github.com/bioc/scPipe", "RemoteRef": "RELEASE_3_23", "RemoteSha": "a390e0028147d43b00179e409f6314750bb49a71", "Packaged": { "Date": "2026-05-30 09:41:32 UTC", "User": "root" }, "Author": "Luyi Tian [aut],\nShian Su [aut, cre],\nShalin Naik [ctb],\nShani Amarasinghe [aut],\nOliver Voogd [aut],\nPhil Yang [aut],\nMatthew Ritchie [ctb]", "Maintainer": "Shian Su ", "MD5sum": "f594c118d75064322c4a63323068aafa", "_user": "bioc-release", "_type": "src", "_file": "scPipe_2.12.0.tar.gz", "_fileid": "ab31a4f550c9c303e718c62f60bfbc9ec9f39831b8e166f4a8e47612736ae891", "_filesize": 13529937, "_sha256": "ab31a4f550c9c303e718c62f60bfbc9ec9f39831b8e166f4a8e47612736ae891", "_created": "2026-05-30T09:41:32.000Z", "_published": "2026-05-30T14:06:25.997Z", "_jobs": [ { "job": 78640434002, "time": 377, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307440343" }, { "job": 78640434039, "time": 506, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7307319089" }, { "job": 78640434047, "time": 627, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307463871" }, { "job": 78640434044, "time": 510, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307319504" }, { "job": 78640434043, "time": 561, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307458329" }, { "job": 78640434026, "time": 534, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308736632" }, { "job": 78640434017, "time": 977, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7307413835" }, { "job": 78640434028, "time": 506, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308733772" }, { "job": 78640434036, "time": 779, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307402325" }, { "job": 78639411403, "time": 712, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307267570" }, { "job": 78640434005, "time": 371, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78640434012, "time": 1077, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307502005" }, { "job": 78640434013, "time": 782, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307477913" }, { "job": 78640434018, "time": 668, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307466858" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scPipe", "_commit": { "id": "a390e0028147d43b00179e409f6314750bb49a71", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380400 }, "_maintainer": { "name": "Shian Su", "email": "su.s@wehi.edu.au", "login": "shians", "description": "Bioinformatician with an interest in high-throughput genomics and epigenomics. Experienced in R and C++.", "uuid": 6036662 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "SingleCellExperiment", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rhtslib", "version": ">= 1.13.1", "role": "LinkingTo" }, { "package": "testthat", "role": "LinkingTo" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "basilisk", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "DropletUtils", "role": "Imports" }, { "package": "flexmix", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glue", "version": ">= 1.3.0", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "hash", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.5.0", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "org.Mm.eg.db", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.11.3", "role": "Imports" }, { "package": "reshape", "role": "Imports" }, { "package": "reticulate", "role": "Imports" }, { "package": "Rhtslib", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "robustbase", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "Rsubread", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vctrs", "version": ">= 0.5.2", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "locStra", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "RANN", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "scater", "version": ">= 1.11.0", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "umap", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.13.1", "bioc": "3.24" }, { "branch": "release", "version": "2.12.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "software", "sequencing", "rnaseq", "geneexpression", "singlecell", "visualization", "sequencematching", "preprocessing", "qualitycontrol", "genomeannotation", "dataimport", "curl", "bzip2", "xz-utils", "zlib", "cpp" ], "_stars": 67, "_contributors": [ { "user": "shians", "count": 442, "uuid": 6036662 }, { "user": "luyitian", "count": 230, "uuid": 3377891 }, { "user": "olivervoogd", "count": 125, "uuid": 51314988 }, { "user": "shaniamare", "count": 79, "uuid": 43805905 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "petehaitch", "count": 8, "uuid": 1049741 }, { "user": "mritchie", "count": 7, "uuid": 965474 }, { "user": "hpages", "count": 6, "uuid": 8810451 }, { "user": "philyang07", "count": 3, "uuid": 48355111 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "hy-yang", "count": 1, "uuid": 52733913 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 485, "source": "https://www.bioconductor.org/packages/stats/bioc/scPipe" }, "_mentions": 7, "_devurl": "https://github.com/luyitian/scpipe", "_searchresults": 90, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/scPipe.html", "manual.pdf" ], "_homeurl": "https://github.com/luyitian/scpipe", "_realowner": "bioc", "_cranurl": false, "_exports": [ "anno_import", "anno_to_saf", "calculate_QC_metrics", "convert_geneid", "create_processed_report", "create_report", "create_sce_by_dir", "demultiplex_info", "demultiplex_info.sce", "demultiplex_info<-", "detect_outlier", "feature_info", "feature_info.sce", "feature_info<-", "feature_type", "feature_type.sce", "feature_type<-", "gene_id_type", "gene_id_type.sce", "gene_id_type<-", "get_ercc_anno", "get_genes_by_GO", "get_read_str", "organism", "organism.sce", "organism<-", "plot_demultiplex", "plot_mapping", "plot_QC_pairs", "plot_UMI_dup", "QC_metrics", "QC_metrics.sce", "QC_metrics<-", "remove_outliers", "sc_aligning", "sc_atac_bam_tagging", "sc_atac_cell_calling", "sc_atac_create_cell_qc_metrics", "sc_atac_create_fragments", "sc_atac_create_report", "sc_atac_create_sce", "sc_atac_emptydrops_cell_calling", "sc_atac_feature_counting", "sc_atac_filter_cell_calling", "sc_atac_peak_calling", "sc_atac_pipeline", "sc_atac_plot_cells_per_feature", "sc_atac_plot_features_per_cell", "sc_atac_plot_features_per_cell_ordered", "sc_atac_plot_fragments_cells_per_feature", "sc_atac_plot_fragments_features_per_cell", "sc_atac_plot_fragments_per_cell", "sc_atac_plot_fragments_per_feature", "sc_atac_remove_duplicates", "sc_atac_tfidf", "sc_atac_trim_barcode", "sc_correct_bam_bc", "sc_count_aligned_bam", "sc_demultiplex", "sc_demultiplex_and_count", "sc_detect_bc", "sc_exon_mapping", "sc_gene_counting", "sc_get_umap_data", "sc_integrate", "sc_interactive_umap_plot", "sc_mae_plot_umap", "sc_trim_barcode", "TF.IDF.custom", "UMI_dup_info", "UMI_dup_info.sce", "UMI_dup_info<-" ], "_datasets": [ { "name": "cell_barcode_matching", "title": "cell barcode demultiplex statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe", "object": "sc_sample_qc", "file": "sc_sample_qc.RData", "class": [ "data.frame" ], "fields": [ "status", "count" ], "rows": 6, "table": true, "tojson": true }, { "name": "sc_sample_data", "title": "a small sample scRNA-seq counts dataset to demonstrate capabilities of scPipe", "object": "sc_sample_data", "file": "sc_sample_data.RData", "class": [ "matrix", "array" ], "fields": [ "A1", "A10", "A11", "A12", "A13", "A14", "A15", "A16", "A17", "A18", "A19", "A2", "A20", "A21", "A22", "A23", "A24", "A3", "A4", "A5", "A6", "A7", "A8", "A9", "B1", "B10", "B11", "B12", "B13", "B14", "B15", "B16", "B17", "B18", "B19", "B2", "B20", "B21", "B22", "B23", "B24", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "C1", "C10", "C11", "C12", "C13", "C14", "C15", "C16", "C17", "C18", "C19", "C2", "C20", "C21", "C22", "C23", "C24", "C3", "C4", "C5", "C6", "C7", "C8", "C9", "D1", "D10", "D11", "D12", "D13", "D14", "D15", "D16", "D17", "D18", "D19", "D2", "D20", "D21", "D22", "D23", "D24", "D3", "D4", "D5", "D6", "D7", "D8", "D9", "E1", "E10", "E11", "E12", "E13", "E14", "E15", "E16", "E17", "E18", "E19", "E2", "E20", "E21", "E22", "E23", "E24", "E3", "E4", "E5", "E6", "E7", "E8", "E9", "F1", "F10", "F11", "F12", "F13", "F14", "F15", "F16", "F17", "F18", "F19", "F2", "F20", "F21", "F22", "F23", "F24", "F3", "F4", "F5", "F6", "F7", "F8", "F9", "G1", "G10", "G11", "G12", "G13", "G14", "G15", "G16", "G17", "G18", "G19", "G2", "G20", "G21", "G22", "G23", "G24", "G3", "G4", "G5", "G6", "G7", "G8", "G9", "H1", "H10", "H11", "H12", "H13", "H14", "H15", "H16", "H17", "H18", "H19", "H2", "H20", "H21", "H22", "H23", "H24", "H3", "H4", "H5", "H6", "H7", "H8", "H9", "I1", "I10", "I11", "I12", "I13", "I14", "I15", "I16", "I17", "I18", "I19", "I2", "I20", "I21", "I22", "I23", "I24", "I3", "I4", "I5", "I6", "I7", "I8", "I9", "J1", "J10", "J11", "J12", "J13", "J14", "J15", "J16", "J17", "J18", "J19", "J2", "J20", "J21", "J22", "J23", "J24", "J3", "J4", "J5", "J6", "J7", "J8", "J9", "K1", "K10", "K11", "K12", "K13", "K14", "K15", "K16", "K17", "K18", "K19", "K2", "K20", "K21", "K22", "K23", "K24", "K3", "K4", "K5", "K6", "K7", "K8", "K9", "L1", "L10", "L11", "L12", "L13", "L14", "L15", "L16", "L17", "L18", "L19", "L2", "L20", "L21", "L22", "L23", "L24", "L3", "L4", "L5", "L6", "L7", "L8", "L9", "M1", "M10", "M11", "M12", "M13", "M14", "M15", "M16", "M17", "M18", "M2", "M20", "M21", "M22", "M23", "M24", "M3", "M4", "M5", "M6", "M7", "M8", "M9", "N1", "N10", "N11", "N12", "N13", "N14", "N15", "N16", "N17", "N18", "N19", "N2", "N20", "N21", "N22", "N23", "N24", "N3", "N4", "N5", "N6", "N7", "N8", "N9", "O1", "O10", "O11", "O12", "O13", "O14", "O15", "O16", "O17", "O18", "O19", "O2", "O20", "O21", "O22", "O23", "O24", "O3", "O4", "O5", "O6", "O7", "O8", "O9", "P1", "P10", "P11", "P12", "P13", "P14", "P15", "P16", "P17", "P18", "P19", "P2", "P20", "P21", "P22", "P23", "P24", "P3", "P4", "P5", "P6", "P7", "P8", "P9" ], "rows": 1000, "table": true, "tojson": true }, { "name": "sc_sample_qc", "title": "quality control information for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe.", "object": "sc_sample_qc", "file": "sc_sample_qc.RData", "class": [ "data.frame" ], "fields": [ "unaligned", "aligned_unmapped", "mapped_to_exon", "mapped_to_intron", "ambiguous_mapping", "mapped_to_ERCC", "mapped_to_MT", "total_count_per_cell", "number_of_genes", "non_ERCC_percent", "non_mt_percent", "non_ribo_percent" ], "rows": 383, "table": true, "tojson": true }, { "name": "UMI_duplication", "title": "UMI duplication statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe", "object": "sc_sample_qc", "file": "sc_sample_qc.RData", "class": [ "data.frame" ], "fields": [ "duplication.number", "count" ], "rows": 1001, "table": true, "tojson": true } ], "_help": [ { "page": "dot-qq_outliers_robust", "title": "Detect outliers based on robust linear regression of QQ plot", "topics": [ ".qq_outliers_robust" ] }, { "page": "anno_import", "title": "Import gene annotation", "topics": [ "anno_import" ] }, { "page": "anno_to_saf", "title": "Convert annotation from GenomicRanges to Simple Annotation Format (SAF)", "topics": [ "anno_to_saf" ] }, { "page": "calculate_QC_metrics", "title": "Calculate QC metrics from gene count matrix", "topics": [ "calculate_QC_metrics" ] }, { "page": "cell_barcode_matching", "title": "cell barcode demultiplex statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe", "topics": [ "cell_barcode_matching" ] }, { "page": "check_barcode_start_position", "title": "Check Valid Barcode Start Position", "topics": [ "check_barcode_start_position" ] }, { "page": "convert_geneid", "title": "convert the gene ids of a SingleCellExperiment object", "topics": [ "convert_geneid" ] }, { "page": "create_processed_report", "title": "create_processed_report", "topics": [ "create_processed_report" ] }, { "page": "create_report", "title": "create_report", "topics": [ "create_report" ] }, { "page": "create_sce_by_dir", "title": "create a SingleCellExperiment object from data folder generated by preprocessing step", "topics": [ "create_sce_by_dir" ] }, { "page": "demultiplex_info", "title": "demultiplex_info", "topics": [ "demultiplex_info", "demultiplex_info,SingleCellExperiment-method", "demultiplex_info.sce", "demultiplex_info<-", "demultiplex_info<-,SingleCellExperiment-method" ] }, { "page": "detect_outlier", "title": "Detect outliers based on QC metrics", "topics": [ "detect_outlier" ] }, { "page": "feature_info", "title": "Get or set 'feature_info' from a SingleCellExperiment object", "topics": [ "feature_info", "feature_info,SingleCellExperiment-method", "feature_info.sce", "feature_info<-", "feature_info<-,SingleCellExperiment-method" ] }, { "page": "feature_type", "title": "Get or set 'feature_type' from a SingleCellExperiment object", "topics": [ "feature_type", "feature_type,SingleCellExperiment-method", "feature_type.sce", "feature_type<-", "feature_type<-,SingleCellExperiment-method" ] }, { "page": "gene_id_type", "title": "Get or set 'gene_id_type' from a SingleCellExperiment object", "topics": [ "gene_id_type", "gene_id_type,SingleCellExperiment-method", "gene_id_type.sce", "gene_id_type<-", "gene_id_type<-,SingleCellExperiment-method" ] }, { "page": "get_chromosomes", "title": "Get Chromosomes", "topics": [ "get_chromosomes" ] }, { "page": "get_ercc_anno", "title": "Get ERCC annotation table", "topics": [ "get_ercc_anno" ] }, { "page": "get_genes_by_GO", "title": "Get genes related to certain GO terms from biomart database", "topics": [ "get_genes_by_GO" ] }, { "page": "get_read_str", "title": "Get read structure for particular scRNA-seq protocol", "topics": [ "get_read_str" ] }, { "page": "organism", "title": "Get or set 'organism' from a SingleCellExperiment object", "topics": [ "organism", "organism,SingleCellExperiment-method", "organism.sce", "organism<-,SingleCellExperiment-method" ] }, { "page": "plot_demultiplex", "title": "plot_demultiplex", "topics": [ "plot_demultiplex" ] }, { "page": "plot_mapping", "title": "Plot mapping statistics for 'SingleCellExperiment' object.", "topics": [ "plot_mapping" ] }, { "page": "plot_QC_pairs", "title": "Plot GGAlly pairs plot of QC statistics from 'SingleCellExperiment' object", "topics": [ "plot_QC_pairs" ] }, { "page": "plot_UMI_dup", "title": "Plot UMI duplication frequency", "topics": [ "plot_UMI_dup" ] }, { "page": "QC_metrics", "title": "Get or set quality control metrics in a SingleCellExperiment object", "topics": [ "QC_metrics", "QC_metrics,SingleCellExperiment-method", "QC_metrics.sce", "QC_metrics<-", "QC_metrics<-,SingleCellExperiment-method" ] }, { "page": "read_cells", "title": "Read Cell barcode file", "topics": [ "read_cells" ] }, { "page": "remove_outliers", "title": "Remove outliers in 'SingleCellExperiment'", "topics": [ "remove_outliers" ] }, { "page": "sc_aligning", "title": "aligning the demultiplexed FASTQ reads using the Rsubread:align()", "topics": [ "sc_aligning" ] }, { "page": "sc_atac_bam_tagging", "title": "BAM tagging", "topics": [ "sc_atac_bam_tagging" ] }, { "page": "sc_atac_cell_calling", "title": "identifying true vs empty cells", "topics": [ "sc_atac_cell_calling" ] }, { "page": "sc_atac_create_cell_qc_metrics", "title": "generating a file useful for producing the qc plots", "topics": [ "sc_atac_create_cell_qc_metrics" ] }, { "page": "sc_atac_create_fragments", "title": "Generating the popular fragments for scATAC-Seq data", "topics": [ "sc_atac_create_fragments" ] }, { "page": "sc_atac_create_report", "title": "HTML report generation", "topics": [ "sc_atac_create_report" ] }, { "page": "sc_atac_create_sce", "title": "sc_atac_create_sce()", "topics": [ "sc_atac_create_sce" ] }, { "page": "sc_atac_emptydrops_cell_calling", "title": "empty drops cell calling", "topics": [ "sc_atac_emptydrops_cell_calling" ] }, { "page": "sc_atac_feature_counting", "title": "generating the feature by cell matrix", "topics": [ "sc_atac_feature_counting" ] }, { "page": "sc_atac_filter_cell_calling", "title": "filter cell calling", "topics": [ "sc_atac_filter_cell_calling" ] }, { "page": "sc_atac_peak_calling", "title": "sc_atac_peak_calling()", "topics": [ "sc_atac_peak_calling" ] }, { "page": "sc_atac_pipeline", "title": "A convenient function for running the entire pipeline", "topics": [ "sc_atac_pipeline" ] }, { "page": "sc_atac_pipeline_quick_test", "title": "A function that tests the pipeline on a small test sample (without duplicate removal)", "topics": [ "sc_atac_pipeline_quick_test" ] }, { "page": "sc_atac_plot_cells_per_feature", "title": "A histogram of the log-number of cells per feature", "topics": [ "sc_atac_plot_cells_per_feature" ] }, { "page": "sc_atac_plot_features_per_cell", "title": "A histogram of the log-number of features per cell", "topics": [ "sc_atac_plot_features_per_cell" ] }, { "page": "sc_atac_plot_features_per_cell_ordered", "title": "Plot showing the number of features per cell in ascending order", "topics": [ "sc_atac_plot_features_per_cell_ordered" ] }, { "page": "sc_atac_plot_fragments_cells_per_feature", "title": "A scatter plot of the log-number of fragments and log-number of cells per feature", "topics": [ "sc_atac_plot_fragments_cells_per_feature" ] }, { "page": "sc_atac_plot_fragments_features_per_cell", "title": "A scatter plot of the log-number of fragments and log-number of features per cell", "topics": [ "sc_atac_plot_fragments_features_per_cell" ] }, { "page": "sc_atac_plot_fragments_per_cell", "title": "A histogram of the log-number of fragments per cell", "topics": [ "sc_atac_plot_fragments_per_cell" ] }, { "page": "sc_atac_plot_fragments_per_feature", "title": "A histogram of the log-number of fragments per feature", "topics": [ "sc_atac_plot_fragments_per_feature" ] }, { "page": "sc_atac_remove_duplicates", "title": "Removing PCR duplicates using samtools", "topics": [ "sc_atac_remove_duplicates" ] }, { "page": "sc_atac_tfidf", "title": "generating the UMAPs for sc-ATAC-Seq preprocessed data", "topics": [ "sc_atac_tfidf" ] }, { "page": "sc_atac_trim_barcode", "title": "demultiplex raw single-cell ATAC-Seq fastq reads", "topics": [ "sc_atac_trim_barcode" ] }, { "page": "sc_correct_bam_bc", "title": "sc_correct_bam_bc", "topics": [ "sc_correct_bam_bc" ] }, { "page": "sc_count_aligned_bam", "title": "sc_count_aligned_bam", "topics": [ "sc_count_aligned_bam" ] }, { "page": "sc_demultiplex", "title": "sc_demultiplex", "topics": [ "sc_demultiplex" ] }, { "page": "sc_demultiplex_and_count", "title": "sc_demultiplex_and_count", "topics": [ "sc_demultiplex_and_count" ] }, { "page": "sc_detect_bc", "title": "sc_detect_bc", "topics": [ "sc_detect_bc" ] }, { "page": "sc_exon_mapping", "title": "sc_exon_mapping", "topics": [ "sc_exon_mapping" ] }, { "page": "sc_gene_counting", "title": "sc_gene_counting", "topics": [ "sc_gene_counting" ] }, { "page": "sc_get_umap_data", "title": "Generates UMAP data from sce object", "topics": [ "sc_get_umap_data" ] }, { "page": "sc_integrate", "title": "Integrate multi-omic scRNA-Seq and scATAC-Seq data into a MultiAssayExperiment", "topics": [ "sc_integrate" ] }, { "page": "sc_interactive_umap_plot", "title": "Produces an interactive UMAP plot via Shiny", "topics": [ "sc_interactive_umap_plot" ] }, { "page": "sc_mae_plot_umap", "title": "Generates UMAP of multiomic data", "topics": [ "sc_mae_plot_umap" ] }, { "page": "sc_sample_data", "title": "a small sample scRNA-seq counts dataset to demonstrate capabilities of scPipe", "topics": [ "sc_sample_data" ] }, { "page": "sc_sample_qc", "title": "quality control information for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe.", "topics": [ "sc_sample_qc" ] }, { "page": "sc_trim_barcode", "title": "sc_trim_barcode", "topics": [ "sc_trim_barcode" ] }, { "page": "scPipe", "title": "scPipe - single cell RNA-seq pipeline", "topics": [ "scPipe-package", "scPipe" ] }, { "page": "TF.IDF.custom", "title": "Returns the TF-IDF normalised version of a binary matrix", "topics": [ "TF.IDF.custom" ] }, { "page": "UMI_dup_info", "title": "Get or set UMI duplication results in a SingleCellExperiment object", "topics": [ "UMI_dup_info", "UMI_dup_info,SingleCellExperiment-method", "UMI_dup_info.sce", "UMI_dup_info<-", "UMI_dup_info<-,SingleCellExperiment-method" ] }, { "page": "UMI_duplication", "title": "UMI duplication statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe", "topics": [ "UMI_duplication" ] } ], "_readme": "https://github.com/bioc/scPipe/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "assorthead", "basilisk", "beachmat", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "brio", "cachem", "callr", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DelayedMatrixStats", "DEoptimR", "desc", "diffobj", "dir.expiry", "dplyr", "dqrng", "DropletUtils", "edgeR", "evaluate", "farver", "fastmap", "filelock", "flexmix", "forcats", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "GGally", "ggplot2", "ggstats", "glue", "gtable", "h5mread", "hash", "HDF5Array", "here", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mime", "modeltools", "MultiAssayExperiment", "nnet", "openssl", "org.Hs.eg.db", "org.Mm.eg.db", "patchwork", "pillar", "pkgbuild", "pkgconfig", "pkgload", "plyr", "png", "praise", "prettyunits", "processx", "progress", "ps", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppTOML", "RCurl", "reshape", "restfulr", "reticulate", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "robustbase", "rprojroot", "Rsamtools", "RSQLite", "Rsubread", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "scuttle", "Seqinfo", "SingleCellExperiment", "sitmo", "snow", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "testthat", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "waldo", "withr", "XML", "xml2", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.5.0-2ubuntu10.9", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libbz2", "package": "libbz2-1.0", "headers": "libbz2-dev", "source": "bzip2", "version": "1.0.8-5.1build0.1", "name": "bzip2", "homepage": "https://sourceware.org/bzip2/", "description": "high-quality block-sorting file compressor library - runtime" }, { "shlib": "liblzma", "package": "liblzma5", "headers": "liblzma-dev", "source": "xz-utils", "version": "5.6.1+really5.4.5-1ubuntu0.2", "name": "xz-utils", "homepage": "https://tukaani.org/xz/", "description": "XZ-format compression library" }, { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "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": "scPipe_tutorial.Rmd", "filename": "scPipe_tutorial.html", "title": "scPipe: a flexible data preprocessing pipeline for 3' end scRNA-seq data", "author": "Luyi Tian", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Case Study: Preprocessing CEL-seq2 data", "Getting started", "Organising the files required", "Data Preprocessing", "Fastq reformatting", "Aligning reads to a reference genome", "Assigning reads to annotated exons", "De-multiplexing data and counting genes", "Preprocessing data generated by other protocols", "Quality Control", "Downstream analysis" ], "created": "2017-03-28 13:18:25", "modified": "2023-10-18 01:05:08", "commits": 24 }, { "source": "scPipe_atac_tutorial.Rmd", "filename": "scPipe_atac_tutorial.html", "title": "scPipe: a flexible data preprocessing pipeline for scATAC-seq data", "author": "Shani Amarasinghe, Phil Yang", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Workflow", "Getting started", "Fastq reformatting", "Aligning reads to a reference genome", "Demultiplexing the BAM file", "Remove duplicates", "Gemerating a fragment file", "Peak calling", "Assigning reads to features and feature counting", "Generating the Single-cell Experiment (SCE) object", "A convenience function for running the whole pipeline", "Downstream analysis", "Session Information" ], "created": "2022-04-22 16:10:12", "modified": "2023-10-05 04:00:37", "commits": 9 } ], "_score": 9.51750995484489, "_indexed": false, "_nocasepkg": "scpipe", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/scPipe", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.12.0", "date": "2026-05-30T09:47:22.000Z", "distro": "noble", "arch": "aarch64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "417d0b955c02438eff2ec547b51c0db31eccaeb09f26c5ce56f15f7d0ca6b1a3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.7.0", "os": "linux", "version": "2.12.0", "date": "2026-05-30T10:12:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "b7151eff21b899b6482646fa81dc09b0749ca93f9c81485176fbdbe1d0e2c46a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.6.0", "os": "linux", "version": "2.12.0", "date": "2026-05-30T09:47:23.000Z", "distro": "noble", "arch": "aarch64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "c1ca3dcc2df08d9e0887b5a200546a4263ce2be8a9c2c1cacd1f34ade93e5633", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.6.0", "os": "linux", "version": "2.12.0", "date": "2026-05-30T10:12:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "b51e6cfe1e1fbbcdf729f406ef796d1c7f7ef77ef0abc23c91750a22ec5848f6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.5.3", "os": "mac", "version": "2.12.0", "date": "2026-05-30T13:59:26.000Z", "arch": "aarch64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "a2a71930ee4f778452d17e0bf31271f60ba37a8ac3f55f416800d5d0fbf500dd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.5.3", "os": "mac", "version": "2.12.0", "date": "2026-05-30T09:56:47.000Z", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "f80750e61c25eaf7d9356a1e4732e68311732c6ba1a6fd3ddf86ea5123acc15b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.6.0", "os": "mac", "version": "2.12.0", "date": "2026-05-30T14:01:53.000Z", "arch": "aarch64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "bcdb3fcab8404aef234a29aed46205605762926fc869bb2ed9d59feb2ddec0b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.6.0", "os": "mac", "version": "2.12.0", "date": "2026-05-30T09:57:40.000Z", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "e1d7c3cf5594dc1d4f4ae07982e579948ef6dc41c27a948bcbb9956d97855b69", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.7.0", "os": "win", "version": "2.12.0", "date": "2026-05-30T10:17:02.000Z", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "971202a543cecf39c380e96ce511999266ba63aba78b2bfca274e5aa894946e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.5.3", "os": "win", "version": "2.12.0", "date": "2026-05-30T10:14:51.000Z", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "88949a45525e65da3e11e2a2ad3cdf578f478e188e8f1099a47e301e659fe4b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" }, { "r": "4.6.0", "os": "win", "version": "2.12.0", "date": "2026-05-30T10:10:19.000Z", "arch": "x86_64", "commit": "a390e0028147d43b00179e409f6314750bb49a71", "fileid": "3d5d08914c3860f9d4389202687682cf20f45d3076bf460b72cb94f21f93f054", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26675548995" } ] }