scPipe

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scPipe.

pipeline for single cell RNA-seq data analysis


Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scPipe")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

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

Details

biocViews GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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, org.Hs.eg.db, org.Mm.eg.db, stringr, rtracklayer, hashmap, dplyr, GenomicRanges, magrittr, glue
System Requirements
URL https://github.com/LuyiTian/scPipe
Bug Reports https://github.com/LuyiTian/scPipe
See More
Suggests Rsubread, knitr, rmarkdown, testthat
Linking To Rcpp, Rhtslib(>= 1.13.1), zlibbioc, testthat
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scPipe_1.6.0.tar.gz
Windows Binary scPipe_1.6.0.zip
Mac OS X 10.11 (El Capitan) scPipe_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scPipe
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scPipe
Bioc Package Browser https://code.bioconductor.org/browse/scPipe/
Package Short Url https://bioconductor.org/packages/scPipe/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive