scCB2
This is the development version of scCB2; for the stable release version, see scCB2.
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
Bioconductor version: Development (3.24)
scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.
Author: Zijian Ni [aut, cre], Shuyang Chen [ctb], Christina Kendziorski [ctb]
Maintainer: Zijian Ni <zni25 at wisc.edu>
citation("scCB2")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scCB2")
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("scCB2")| CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | R (>= 3.6.0) |
| Imports | SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat |
| System Requirements | C++11 |
| URL | https://github.com/zijianni/scCB2 |
| Bug Reports | https://github.com/zijianni/scCB2/issues |
See More
| Suggests | testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown |
| 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 | scCB2_1.23.0.tar.gz |
| Windows Binary (x86_64) | scCB2_1.23.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | scCB2_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | scCB2_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scCB2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scCB2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scCB2/ |
| Package Short Url | https://bioconductor.org/packages/scCB2/ |
| Package Downloads Report | Download Stats |