scrapper
This is the development version of scrapper; for the stable release version, see scrapper.
Bindings to C++ Libraries for Single-Cell Analysis
Bioconductor version: Development (3.24)
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")):Aaron Lun. scrapper: Bindings to C++ Libraries for Single-Cell Analysis. doi:10.18129/B9.bioc.scrapper, R package version 1.7.9, https://bioconductor.org/packages/scrapper.
Generated from the package metadata; it may differ from the package's own citation.
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("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")| Link to book | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, Clustering, DifferentialExpression, FeatureExtraction, GeneExpression, Normalization, PrincipalComponent, QualityControl, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.7.9 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | stats, 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, igraph |
| Linking To | Rcpp, assorthead (>= 1.5.16), beachmat, BiocNeighbors, Rigraphlib |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.multisample, scrapbook, SingleRBook |
| Imports Me | augere.solo, BatChef, decontX, epiregulon, FLAMES, imcRtools, muscat, OSTA, scBatchQC, scDblFinder, singleCellTK, spatialLIBD, splatter |
| Suggests Me | alabaster.matrix, bluster, Coralysis, epiregulon.extra, GSVA, iSEE, iSEEid, OSTA, raer, ReactomeGSA, scran, SingleR, sketchR, SpatialFeatureExperiment, spatialHeatmap, TabulaMurisData, Voyager |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scrapper_1.7.9.tar.gz |
| Windows Binary (x86_64) | scrapper_1.7.9.zip |
| macOS Binary (big-sur-x86_64) | scrapper_1.7.9.tgz |
| macOS Binary (sonoma-arm64) | scrapper_1.7.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scrapper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scrapper |
| Package Short Url | https://bioconductor.org/packages/scrapper/ |
| Package Downloads Report | Download Stats |