{ "_id": "6a168de9acfb0bcc41d779a6", "Package": "BUSpaRse", "Type": "Package", "Title": "kallisto | bustools R utilities", "Version": "1.27.0", "Date": "2025-09-15", "Authors@R": "c(person(\"Lambda\", \"Moses\", email = \"dl3764@columbia.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7092-9427\")),\nperson(\"Lior\", \"Pachter\", email = \"lpachter@caltech.edu\",\nrole = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0002-9164-6231\")))", "Description": "The kallisto | bustools pipeline is a fast and modular set\nof tools to convert single cell RNA-seq reads in fastq files\ninto gene count or transcript compatibility counts (TCC)\nmatrices for downstream analysis. Central to this pipeline is\nthe barcode, UMI, and set (BUS) file format. This package\nserves the following purposes: First, this package allows users\nto manipulate BUS format files as data frames in R and then\nconvert them into gene count or TCC matrices. Furthermore,\nsince R and Rcpp code is easier to handle than pure C++ code,\nusers are encouraged to tweak the source code of this package\nto experiment with new uses of BUS format and different ways to\nconvert the BUS file into gene count matrix. Second, this\npackage can conveniently generate files required to generate\ngene count matrices for spliced and unspliced transcripts for\nRNA velocity. Here biotypes can be filtered and scaffolds and\nhaplotypes can be removed, and the filtered transcriptome can\nbe extracted and written to disk. Third, this package\nimplements utility functions to get transcripts and associated\ngenes required to convert BUS files to gene count matrices, to\nwrite the transcript to gene information in the format required\nby bustools, and to read output of bustools into R as sparses\nmatrices.", "BugReports": "https://github.com/BUStools/BUSpaRse/issues", "URL": "https://github.com/BUStools/BUSpaRse", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "LazyData": "TRUE", "Collate": "'RcppExports.R' 'annots_from_fa.R' 'biotypes.R' 'get_tx.R'\n'knee_plot.R' 'sparse_matrix.R' 'tr2g.R' 'utils.R' 'velocity.R'\n'velocity_methods.R'", "Encoding": "UTF-8", "License": "BSD_2_clause + file LICENSE", "biocViews": "SingleCell, RNASeq, WorkflowStep", "SystemRequirements": "GNU make", "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": "2026-04-28 12:50:47 UTC", "RemoteUrl": "https://github.com/bioc/BUSpaRse", "RemoteRef": "HEAD", "RemoteSha": "b35dd0b3fd69c36057496007d6ba89a9acb35dc2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-25 06:18:25 UTC", "User": "root" }, "Author": "Lambda Moses [aut, cre] (ORCID:\n),\nLior Pachter [aut, ths] (ORCID:\n)", "Maintainer": "Lambda Moses ", "MD5sum": "9c07d18530d823b9a5225e7dc54c2f31", "_user": "bioc", "_type": "src", "_file": "BUSpaRse_1.27.0.tar.gz", "_fileid": "f37c033d16fbe35ba4e2e2812ed6308bd5aab8f773803d8f51ff52007f9b0886", "_filesize": 456933, "_sha256": "f37c033d16fbe35ba4e2e2812ed6308bd5aab8f773803d8f51ff52007f9b0886", "_created": "2026-05-25T06:18:25.000Z", "_published": "2026-05-27T06:23:37.864Z", "_jobs": [ { "job": 78016506100, "time": 348, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7192808782" }, { "job": 78016505919, "time": 1647, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7233323802" }, { 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