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scPipe (development version)

scPipe

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

Pipeline for single cell multi-omic data pre-processing

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DOI: 10.18129/B9.bioc.scPipe

Bioconductor version: Development (3.23)

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 "4.6") 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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization

Version 2.11.0

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

See More

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_2.11.0.tar.gz

Windows Binary (x86_64)

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

Bioc Package Browser https://code.bioconductor.org/browse/scPipe/

Package Short Url https://bioconductor.org/packages/scPipe/

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