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
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)
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
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
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