scPipe
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see scPipe.
pipeline for single cell RNA-seq data analysis
Bioconductor version: 3.10
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 "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization |
| Version | 1.8.0 |
| 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 | C++11, GNU make |
| 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_1.8.0.tar.gz |
| Windows Binary | scPipe_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | scPipe_1.8.0.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 3.10 | Source Archive |