scmap

DOI: 10.18129/B9.bioc.scmap    

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

Bioconductor version: Release (3.7)

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 (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

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

Details

biocViews Classification, DataImport, DataRepresentation, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, SupportVectorMachine, Transcription, Transcriptomics, Visualization
Version 1.2.0
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_1.2.0.tar.gz
Windows Binary scmap_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scmap_1.2.0.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 http://bioconductor.org/packages/scmap/
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