SCMarker-package: What the package does (short line)
In Fang0828/SCMarker: What the package does (short line)

Description Details Author(s) References See Also Examples

SCMarker is about marker selection on single cell RNA sequenceing data. This package implement the marker selection algorithm developed by Fang Wang. It provides the user with tools for generating features to further clustering. This is done based on two hypotheses. One is that gene should follow bi/multi-modal distribution in a mixed cell population if it is a marker of a specific cell type. The second is that genes which are the markers of the same cell type should co-express in the same cells and mutually exclusive with genes which are markers of different cell type.

Package:	SCMarker
Type:	Package
Version:	2.0
Date:	2018-09-04
License:	GPL(>=2)

Fang Wang

Maintainer: Fang Wang <fwang9@mdanderson.org>,<wfang0828@gmail.com>

~~ Literature or other references for background information ~~

~~ Optional links to other man pages, e.g. ~~ ~~ <pkg> ~~

data(melanoma)
melanoma1=as.matrix(melanoma[,2:dim(melanoma)[2]])
row.names(melanoma1)=melanoma[,1]
res=ModalFilter(data=melanoma1,geneK=10,cellK=10,width=2)
res=GeneFilter(obj=res)
res=getMarker(obj=res,MNN=300,MNNIndex=30)
library(Seurat)
library(SC3)
library(dbscan)
library(dplyr)
res=SCcluster(obj=res)
res=getClusterGene(obj=res,method="Seurat")
HeatmapCluster(obj=res,top=10)
HeatmapCell(obj=res,5)