DOI: 10.18129/B9.bioc.scPipe    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see scPipe.

pipeline for single cell RNA-seq data analysis

Bioconductor version: 3.7

A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene 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

Maintainer: Luyi Tian <tian.l at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



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


biocViews GeneExpression, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version 1.2.1
License GPL (>= 2)
Depends R (>= 3.4), ggplot2, methods, SingleCellExperiment
Imports Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment, AnnotationDbi,,
LinkingTo Rcpp, Rhtslib(>= 1.12.1), zlibbioc
Suggests knitr, rmarkdown, testthat
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scPipe_1.2.1.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scPipe_1.2.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: