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This is the development version of scPipe; for the stable release version, see scPipe.

Pipeline for single cell multi-omic data pre-processing

Bioconductor version: Development (3.20)

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.

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 at>

Citation (from within R, enter citation("scPipe")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

scPipe: a flexible data preprocessing pipeline for 3' end scRNA-seq data HTML R Script
scPipe: a flexible data preprocessing pipeline for scATAC-seq data HTML R Script
Reference Manual PDF


biocViews DataImport, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version 2.5.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 2)
Depends R (>= 4.2.0), SingleCellExperiment
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,,, 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)
System Requirements C++11, GNU make
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Suggests BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater(>= 1.11.0), testthat, xml2, umap
Linking To Rcpp, Rhtslib(>= 1.13.1), zlibbioc, testthat
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Source Package scPipe_2.5.0.tar.gz
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macOS Binary (x86_64) scPipe_2.5.0.tgz
macOS Binary (arm64) scPipe_2.5.0.tgz
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