scPipe

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 wehi.edu.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scPipe")

Documentation

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

browseVignettes("scPipe")

 

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

Details

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, org.Hs.eg.db, org.Mm.eg.db
LinkingTo	Rcpp, Rhtslib(>= 1.12.1), zlibbioc
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/LuyiTian/scPipe
BugReports	https://github.com/LuyiTian/scPipe
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	scPipe_1.2.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	scPipe_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scPipe
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scPipe
Package Short Url	http://bioconductor.org/packages/scPipe/
Package Downloads Report	Download Stats