scPipe

DOI: 10.18129/B9.bioc.scPipe    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scPipe.

pipeline for single cell RNA-seq data analysis

Bioconductor version: 3.12

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 (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.6 (R-3.4) (3.5 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, 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
Enhances
URL	https://github.com/LuyiTian/scPipe
BugReports	https://github.com/LuyiTian/scPipe
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	scPipe_1.12.0.tar.gz
Windows Binary	scPipe_1.12.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	scPipe_1.12.0.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