scrapper
This is the released version of scrapper; for the devel version, see scrapper.
Bindings to C++ Libraries for Single-Cell Analysis
Bioconductor version: Release (3.23)
Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. Additional wrappers are provided for easy construction of end-to-end workflows involving Bioconductor objects like SingleCellExperiments.
Author: Aaron Lun [cre, aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("scrapper")):
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")
BiocManager::install("scrapper")
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("scrapper")| Using scrapper to analyze single-cell data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, Clustering, DifferentialExpression, FeatureExtraction, GeneExpression, Normalization, PrincipalComponent, QualityControl, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.6.3 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | methods, Rcpp, beachmat(>= 2.25.1), S4Vectors, SparseArray, DelayedArray, BiocNeighbors(>= 1.99.0), parallel |
| System Requirements | C++17, GNU make |
| URL | https://github.com/libscran/scrapper |
| Bug Reports | https://github.com/libscran/scrapper/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, Matrix, IRanges, SummarizedExperiment, SingleCellExperiment, scRNAseq, org.Mm.eg.db, scater, igraph |
| Linking To | Rcpp, assorthead(>= 1.5.16), beachmat, BiocNeighbors, Rigraphlib |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, scrapbook, SingleRBook |
| Imports Me | BatChef, epiregulon, FLAMES, imcRtools, scDblFinder, splatter, OSTA |
| Suggests Me | Coralysis, GSVA, scran, SingleR, spatialHeatmap, OSTA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scrapper_1.6.3.tar.gz |
| Windows Binary (x86_64) | scrapper_1.6.3.zip |
| macOS Binary (big-sur-x86_64) | scrapper_1.5.17.tgz |
| macOS Binary (sonoma-arm64) | scrapper_1.6.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scrapper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scrapper |
| Bioc Package Browser | https://code.bioconductor.org/browse/scrapper/ |
| Package Short Url | https://bioconductor.org/packages/scrapper/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |