scmap
This is the development version of scmap; for the stable release version, see scmap.
A tool for unsupervised projection of single cell RNA-seq data
Bioconductor version: Development (3.24)
Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.
Author: Vladimir Kiselev
Maintainer: Vladimir Kiselev <vladimir.yu.kiselev at gmail.com>
citation("scmap")):Vladimir Kiselev. scmap: A tool for unsupervised projection of single cell RNA-seq data. doi:10.18129/B9.bioc.scmap, R package version 1.35.0, https://bioconductor.org/packages/scmap.
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("scmap")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("scmap")| `scmap` package vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Sequencing, SingleCell, Software, SupportVectorMachine, Transcription, Transcriptomics, Visualization |
| Version | 1.35.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.4) |
| Imports | Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) |
| System Requirements | |
| URL | https://github.com/hemberg-lab/scmap |
| Bug Reports | https://support.bioconductor.org/t/scmap/ |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scmap_1.35.0.tar.gz |
| Windows Binary (x86_64) | scmap_1.35.0.zip |
| macOS Binary (big-sur-x86_64) | scmap_1.35.0.tgz |
| macOS Binary (sonoma-arm64) | scmap_1.35.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scmap |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scmap |
| Package Short Url | https://bioconductor.org/packages/scmap/ |
| Package Downloads Report | Download Stats |