To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scmap")

In most cases, you don't need to download the package archive at all.

scmap

DOI: 10.18129/B9.bioc.scmap    

This is the development version of scmap; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.6)

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 identified in a different experiment.

Author: Vladimir Kiselev

Maintainer: Vladimir Kiselev <vladimir.yu.kiselev at gmail.com>

Citation (from within R, enter citation("scmap")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scmap")

Documentation

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

Details

biocViews Classification, DataImport, DataRepresentation, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, SupportVectorMachine, Transcription, Transcriptomics, Visualization
Version 0.99.5
In Bioconductor since BioC 3.6 (R-3.4)
License GPL-3
Depends R (>= 3.4)
Imports Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest
LinkingTo
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
Build Report  

Package Archives

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

Package Source scmap_0.99.5.tar.gz
Windows Binary scmap_0.99.5.zip
Mac OS X 10.11 (El Capitan) scmap_0.99.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/scmap
Package Short Url http://bioconductor.org/packages/scmap/
Package Downloads Report Download Stats

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