scPipe
This is thereleased version of scPipe; for the devel version, seescPipe.
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("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 appropriateBioconductor 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 | 2.10.0 |
| 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | scPipe_2.10.0.tar.gz |
| Windows Binary (x86_64) | scPipe_2.10.0.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 git@git.bioconductor.org:packages/scPipe |
| Bioc Package Browser | https://code.bioconductor.org/browse/scPipe/ |
| Package Short Url | https://bioconductor.org/packages/scPipe/ |
| Package Downloads Report | Download Stats |