{"id":13592855,"url":"https://github.com/KChen-lab/SCMarker","last_synced_at":"2025-04-09T02:31:40.166Z","repository":{"id":155325644,"uuid":"138614038","full_name":"KChen-lab/SCMarker","owner":"KChen-lab","description":"Marker gene selection from scRNA-seq 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packages"],"sub_categories":["RNA-seq","Marker and differential gene expression identification"],"readme":"# SCMarker\n\nSCMarker performs cell-type-specific marker selection from single cell RNA sequencing data.\nIt provides users a tool for selecting features from tens of thousands of genes for further cell-type clustering analysis.\n\nSCMarker is done based on two hypotheses:\n1) The expression of a gene should follow bi/multi-modal distribution in a mixed cell population if it is a marker of a specific cell-type.\n2) Marker genes of a cell type express synergistically in a subset of cells.\n\nDeveloper\n------------\nFang Wang (fwang9@outlook.com)\n\n\nMarker selection\n---------------------\nThe three main functions for this package are `ModalFilter()`, `GeneFilter()` and `getMarker()`.\n\n`ModalFilter()` performs the initial filter based on the least expressed number of genes(cells) and whether the gene has unimodal distribution.\n\n`GeneFilter()` takes the output of ModalFilter() and filters out genes that have unimodal distributed expressions and are expressed in more than maxexp cells.\n\n`getMarker()` takes the output of GeneFilter() and selects the final markers based on synergistically (co- or mutual-exclusively) expressed gene pairs.\n\n\n\nInstallation\n----------------------\nDownload SCMarker_2.0.tar.gz\n```R\ninstall.packages(\"SCMarker_2.0.tar.gz\",repos=NULL,type=\"source\")\n```\nor install through GitHub\n```R\nlibrary(devtools)\ninstall_github(\"KChen-lab/SCMarker\")\n```\n\n\nUsage\n----------------------\n\n```R\nlibrary(SCMarker)\ndata(melanoma)\nmelanoma1=as.matrix(melanoma[,2:dim(melanoma)[2]])\nrow.names(melanoma1)=melanoma[,1]\nres=ModalFilter(data=melanoma1,geneK=10,cellK=10,width=2)# default width = 1 for UMI data, width =2 for TPM data.\nres=GeneFilter(obj=res)\nres=getMarker(obj=res,k=300,n=30)\nhead(res$marker)\n\n```\n\nAn example to show how SCMarker [improve identification of NK cell in GBM data.](https://github.com/KChen-lab/SCMarker/blob/master/test/NK%20cell%20identification%20from%20GBM%20data.pdf)\n\nPublication\n-----------------------\nWang, Fang, et al. \"SCMarker: ab initio marker selection for single cell transcriptome profiling.\" PLoS computational biology 15.10 (2019): e1007445.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FKChen-lab%2FSCMarker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FKChen-lab%2FSCMarker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FKChen-lab%2FSCMarker/lists"}