DOI: 10.18129/B9.bioc.scPipe    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scPipe.

pipeline for single cell RNA-seq data analysis

Bioconductor version: 3.11

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")):


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biocViews GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.6 (R-3.4) (3 years)
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,,, stringr, rtracklayer, hash, dplyr, GenomicRanges, magrittr, glue (>= 1.3.0), rlang, scater(>= 1.11.0)
LinkingTo Rcpp, Rhtslib(>= 1.13.1), zlibbioc, testthat
Suggests Rsubread, knitr, rmarkdown, testthat
SystemRequirements C++11, GNU make
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