scPipe

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see scPipe.

pipeline for single cell RNA-seq data analysis

Bioconductor version: 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 wehi.edu.au>

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization

Version 1.0.6

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

System Requirements

URL https://github.com/LuyiTian/scPipe

Bug Reports https://github.com/LuyiTian/scPipe

Suggests knitr, rmarkdown, testthat

Linking To Rcpp, Rhtslib, zlibbioc

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_1.0.6.tar.gz

Windows Binary scPipe_1.0.6.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) scPipe_1.0.6.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 https://bioconductor.org/packages/scPipe/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.6 Source Archive