scPipe: pipeline for single cell RNA-seq data analysis

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.

Package details

AuthorLuyi Tian
Bioconductor views GeneExpression GenomeAnnotation ImmunoOncology Preprocessing QualityControl RNASeq SequenceMatching Sequencing SingleCell Software Visualization
MaintainerLuyi Tian <>
LicenseGPL (>= 2)
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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scPipe documentation built on Nov. 8, 2020, 8:28 p.m.