Package: scPipe
Title: Pipeline for single cell multi-omic data pre-processing
Date: 2022-10-12
Version: 2.11.0
Type: Package
Authors@R: c(person("Luyi", "Tian", role=c("aut"), email="tian.l@wehi.edu.au"), 
        person("Shian", "Su", role=c("aut", "cre"), email="su.s@wehi.edu.au"), 
        person("Shalin", "Naik", role=c("ctb"), email="naik.s@wehi.edu.au"), 
        person("Shani", "Amarasinghe", role=c("aut"), email="amarasinghe.s@wehi.edu.au"), 
        person("Oliver", "Voogd", role=c("aut"), email="voogd.o@wehi.edu.au"), 
        person("Phil", "Yang", role=c("aut"), email="yang.p@wehi.edu.au"), 
        person("Matthew", "Ritchie", role=c("ctb"), email="mritchie@wehi.edu.au"))
biocViews: ImmunoOncology, Software, Sequencing, RNASeq,
        GeneExpression, SingleCell, Visualization, SequenceMatching,
        Preprocessing, QualityControl, GenomeAnnotation, DataImport
Description: A preprocessing pipeline for single cell RNA-seq/ATAC-seq
        data that starts from the fastq files and produces a feature
        count matrix with associated quality control information. It
        can process fastq data generated by CEL-seq, MARS-seq,
        Drop-seq, Chromium 10x and SMART-seq protocols.
Depends: R (>= 4.2.0), SingleCellExperiment
LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat
Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings,
        data.table, dplyr, DropletUtils, flexmix, GenomicRanges,
        GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices,
        graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0),
        mclust, methods, MultiAssayExperiment, org.Hs.eg.db,
        org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate,
        Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer,
        SummarizedExperiment, S4Vectors, scales, stats, stringr,
        tibble, tidyr, tools, utils, vctrs (>= 0.5.2)
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
Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra,
        knitr, locStra, plotly, rmarkdown, RColorBrewer, readr,
        reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev python3 xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:41:32 UTC
RemoteUrl: https://github.com/bioc/scPipe
RemoteRef: HEAD
RemoteSha: fbfb46419bcf08e88a80ea729c54cfcdbbf5f052
Packaged: 2026-03-04 09:19:15 UTC; root
Author: Luyi Tian [aut],
  Shian Su [aut, cre],
  Shalin Naik [ctb],
  Shani Amarasinghe [aut],
  Oliver Voogd [aut],
  Phil Yang [aut],
  Matthew Ritchie [ctb]
Maintainer: Shian Su <su.s@wehi.edu.au>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-03-09 11:05:20 UTC; windows
Archs: x64
