scmap

DOI: 10.18129/B9.bioc.scmap    

A tool for unsupervised projection of single cell RNA-seq data

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	`scmap` package vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Sequencing, SingleCell, Software, SupportVectorMachine, Transcription, Transcriptomics, Visualization
Version	1.18.0
In Bioconductor since	BioC 3.6 (R-3.4) (5 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)
LinkingTo	Rcpp, RcppArmadillo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/hemberg-lab/scmap
BugReports	https://support.bioconductor.org/t/scmap/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scmap_1.18.0.tar.gz
Windows Binary	scmap_1.18.0.zip
macOS Binary (x86_64)	scmap_1.18.0.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