scPipe

DOI: 10.18129/B9.bioc.scPipe    

This is the development version of scPipe; for the stable release version, see scPipe.

pipeline for single cell RNA-seq data analysis

Bioconductor version: Development (3.17)

A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature 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 [aut], Shian Su [aut], Shalin Naik [ctb], Shani Amarasinghe [aut], Oliver Voogd [aut], Phil Yang [aut, cre], Matthew Ritchie [ctb]

Maintainer: ERROR

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scPipe")

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

Documentation

PDF		Reference Manual

Details

biocViews	GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version	1.21.0
In Bioconductor since	BioC 3.6 (R-3.4) (5 years)
License	GPL (>= 2)
Depends	R (>= 3.5), SingleCellExperiment
Imports	GenomicFeatures, GenomicRanges, SummarizedExperiment, AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grid, hash, IRanges, locStra, magrittr, MASS, Matrix, mclust, methods, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, S4Vectors, scales, scater(>= 1.11.0), SingleCellExperiment, stats, stringr, tibble, tidyr, tools, utils
LinkingTo	Rcpp, Rhtslib(>= 1.13.1), zlibbioc, testthat
Suggests	knitr, rmarkdown, testthat, xml2, countreg, flexmix, kableExtra, RColorBrewer, DT
SystemRequirements	C++11, GNU make
Enhances
URL	https://github.com/LuyiTian/scPipe
BugReports	https://github.com/LuyiTian/scPipe
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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