scPipe

This is the released version of scPipe; for the devel version, see scPipe.

Pipeline for single cell multi-omic data pre-processing

Bioconductor version: Release (3.22)

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, cre], Shalin Naik [ctb], Shani Amarasinghe [aut], Oliver Voogd [aut], Phil Yang [aut], Matthew Ritchie [ctb]

Maintainer: Shian Su <su.s at wehi.edu.au>

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

Installation

To install this package, start R (version "4.5") 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: a flexible data preprocessing pipeline for 3' end scRNA-seq data	HTML	R Script
scPipe: a flexible data preprocessing pipeline for scATAC-seq data	HTML	R Script
Reference Manual	PDF
NEWS	Text

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Details

biocViews	DataImport, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization
Version	2.10.0
In Bioconductor since	BioC 3.6 (R-3.4) (8 years)
License	GPL (>= 2)
Depends	R (>= 4.2.0), SingleCellExperiment
Imports	AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2)
System Requirements	C++11, GNU make
URL	https://github.com/LuyiTian/scPipe
Bug Reports	https://github.com/LuyiTian/scPipe

Suggests	BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater(>= 1.11.0), testthat, xml2, umap
Linking To	Rcpp, Rhtslib(>= 1.13.1), testthat
Enhances
Depends On Me
Imports Me	stPipe
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_2.10.0.tar.gz
Windows Binary (x86_64)	scPipe_2.9.0.zip (64-bit only)
macOS Binary (x86_64)	scPipe_2.10.0.tgz
macOS Binary (arm64)	scPipe_2.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scPipe
Source Repository (Developer Access)	git clone [email protected]:packages/scPipe
Bioc Package Browser	https://code.bioconductor.org/browse/scPipe/
Package Short Url	https://bioconductor.org/packages/scPipe/
Package Downloads Report	Download Stats