scPipe
Pipeline for single cell multi-omic data pre-processing
Bioconductor version: 3.23 · Package version: 2.12.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scPipe")Details
| Maintainer | Shian Su <su.s@wehi.edu.au> |
| Author | Luyi Tian [aut], Shian Su [aut, cre], Shalin Naik [ctb], Shani Amarasinghe [aut], Oliver Voogd [aut], Phil Yang [aut], Matthew Ritchie [ctb] |
| License | GPL (>= 2) |
| URL | https://github.com/LuyiTian/scPipe |
| Bug Reports | https://github.com/LuyiTian/scPipe |
| System Requirements | C++11, GNU make |
| Downloads rank | 423 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Visualization |
Documentation
- scPipe: a flexible data preprocessing pipeline for 3' end scRNA-seq data
- scPipe: a flexible data preprocessing pipeline for scATAC-seq data
Download
Dependencies
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)
LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat
Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap
Reverse dependencies
Imports Me (1): stPipe