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Pipeline for single cell multi-omic data pre-processing

Bioconductor version: Release (3.19)

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))


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 2.4.0
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_2.4.0.tar.gz
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