scruff
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scruff.
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Bioconductor version: 3.12
A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.
Author: Zhe Wang [aut, cre], Junming Hu [aut], Joshua Campbell [aut]
Maintainer: Zhe Wang <zhe at bu.edu>
citation("scruff")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scruff")
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("scruff")| Process Single Cell RNA-Seq reads using scruff | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Technology, Visualization, WorkflowStep |
| Version | 1.8.3 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/campbio/scruff/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| 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 | scruff_1.8.3.tar.gz |
| Windows Binary | scruff_1.8.3.zip |
| macOS 10.13 (High Sierra) | scruff_1.8.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scruff |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scruff |
| Bioc Package Browser | https://code.bioconductor.org/browse/scruff/ |
| Package Short Url | https://bioconductor.org/packages/scruff/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |