DOI: 10.18129/B9.bioc.scPipe    

pipeline for single cell RNA-seq data analysis

Bioconductor version: Release (3.6)

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>

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HTML R Script scPipe: flexible data preprocessing pipeline for 3' end scRNA-seq data
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biocViews GeneExpression, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version 1.0.6
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
LinkingTo Rcpp, Rhtslib, zlibbioc
Suggests knitr, rmarkdown, testthat
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Source Package scPipe_1.0.6.tar.gz
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