This package is for version 3.16 of Bioconductor;
for the stable, up-to-date release version, see
scPipe.
Pipeline for single cell multi-omic data pre-processing
Bioconductor version: 3.16
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 "4.2") 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
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scPipe: a flexible data preprocessing pipeline for single-cell data
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Details
biocViews
DataImport,
GeneExpression,
GenomeAnnotation,
ImmunoOncology,
Preprocessing,
QualityControl,
RNASeq,
SequenceMatching,
Sequencing,
SingleCell,
Software,
Visualization
Version
1.20.6
In Bioconductor since
BioC 3.6 (R-3.4) (6.5 years)
License
GPL (>= 2)
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
System Requirements
C++11, GNU make
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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/scPipe
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/scPipe