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>
citation("scPipe")
):
Installation
To install this package, start R (version "3.5") 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 | ||
NEWS | Text |
Details
biocViews | GeneExpression, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization |
Version | 1.2.1 |
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 |
System Requirements | |
URL | https://github.com/LuyiTian/scPipe |
Bug Reports | https://github.com/LuyiTian/scPipe |
See More
Suggests | knitr, rmarkdown, testthat |
Linking To | Rcpp, Rhtslib(>= 1.12.1), 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_1.2.1.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 | https://bioconductor.org/packages/scPipe/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |