scPipe
This is the development version of scPipe; for the stable release version, see scPipe.
Pipeline for single cell multi-omic data pre-processing
Bioconductor version: Development (3.21)
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("scPipe")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization |
| Version | 2.7.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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), zlibbioc, testthat |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_2.7.0.tar.gz |
| Windows Binary (x86_64) | scPipe_2.7.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |