Package: BUSpaRse
Type: Package
Title: kallisto | bustools R utilities
Version: 1.24.0
Date: 2025-09-15
Authors@R: 
    c(person("Lambda", "Moses", email = "dl3764@columbia.edu", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-7092-9427")),
    person("Lior", "Pachter", email = "lpachter@caltech.edu",
    role = c("aut", "ths"),
    comment = c(ORCID = "0000-0002-9164-6231")))
Description: The kallisto | bustools pipeline is a fast and modular set
        of tools to convert single cell RNA-seq reads in fastq files
        into gene count or transcript compatibility counts (TCC)
        matrices for downstream analysis. Central to this pipeline is
        the barcode, UMI, and set (BUS) file format. This package
        serves the following purposes: First, this package allows users
        to manipulate BUS format files as data frames in R and then
        convert them into gene count or TCC matrices. Furthermore,
        since R and Rcpp code is easier to handle than pure C++ code,
        users are encouraged to tweak the source code of this package
        to experiment with new uses of BUS format and different ways to
        convert the BUS file into gene count matrix. Second, this
        package can conveniently generate files required to generate
        gene count matrices for spliced and unspliced transcripts for
        RNA velocity. Here biotypes can be filtered and scaffolds and
        haplotypes can be removed, and the filtered transcriptome can
        be extracted and written to disk. Third, this package
        implements utility functions to get transcripts and associated
        genes required to convert BUS files to gene count matrices, to
        write the transcript to gene information in the format required
        by bustools, and to read output of bustools into R as sparses
        matrices.
BugReports: https://github.com/BUStools/BUSpaRse/issues
URL: https://github.com/BUStools/BUSpaRse
Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, biomaRt,
        BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb,
        GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges,
        lifecycle, magrittr, Matrix, methods, plyranges, Rcpp,
        S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker,
        TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene,
        BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
VignetteBuilder: knitr
LazyData: TRUE
Collate: 'RcppExports.R' 'annots_from_fa.R' 'biotypes.R' 'get_tx.R'
        'knee_plot.R' 'sparse_matrix.R' 'tr2g.R' 'utils.R' 'velocity.R'
        'velocity_methods.R'
Encoding: UTF-8
License: BSD_2_clause + file LICENSE
biocViews: SingleCell, RNASeq, WorkflowStep
SystemRequirements: GNU make
Depends: R (>= 3.6)
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:53:52 UTC
RemoteUrl: https://github.com/bioc/BUSpaRse
RemoteRef: RELEASE_3_22
RemoteSha: 757e3e4aefa5deb3b2adf937e3c8b10249037dfd
NeedsCompilation: yes
Packaged: 2025-11-11 13:35:01 UTC; root
Author: Lambda Moses [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7092-9427>),
  Lior Pachter [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-9164-6231>)
Maintainer: Lambda Moses <dl3764@columbia.edu>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 13:45:29 UTC; windows
Archs: x64
