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 (3.22)
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. It is mostly intended for other Bioconductor package developers to build more user-friendly end-to-end workflows.
Author: Aaron Lun [cre, aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("scrapper")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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")| 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 | 1.3.19 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | methods, Rcpp, beachmat(>= 2.25.1), DelayedArray, BiocNeighbors(>= 1.99.0), Rigraphlib, parallel |
| System Requirements | C++17, GNU make |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment, SingleCellExperiment, scRNAseq, igraph |
| Linking To | Rcpp, assorthead(>= 1.3.10), beachmat, BiocNeighbors |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, SingleRBook |
| Imports Me | epiregulon |
| Suggests Me | Coralysis, SingleR, OSTA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scrapper_1.3.19.tar.gz |
| Windows Binary (x86_64) | scrapper_1.3.6.zip (64-bit only) |
| macOS Binary (x86_64) | scrapper_1.3.19.tgz |
| macOS Binary (arm64) | scrapper_1.3.19.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 |