scMAGeCK-package: Identify genes associated with multiple expression phenotypes...

In scMAGeCK: Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

Description

scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (CROP-seq)

Details

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scMAGeCK is a computational model to identify genes associated with multiple expression phenotypes from CRISPR screening coupled with single-cell RNA sequencing data (CROP-seq).scMAGeCK is based on our previous MAGeCK and MAGeCK-VISPR models for pooled CRISPR screens.

The scMAGeCK manuscript can be found at bioRxiv(https://www.biorxiv.org/content/10.1101/658146v1/).

Author(s)

Wei Li, Xiaolong Cheng

Maintainer: Xiaolong Cheng <[e-mail]>

Examples

    ### BARCODE file contains cell identity information, generated from 
    ### the cell identity collection step
    BARCODE <- system.file("extdata","barcode_rec.txt",package = "scMAGeCK")
    ### RDS can be a Seurat object or local RDS file path that contains 
    ### the scRNA-seq dataset
    RDS <- system.file("extdata","singles_dox_mki67_v3.RDS",package = "scMAGeCK")
    
    ### Set RRA executable file path. 
    ###   You can generate RRA executable file by following commands:
    ###   wget https://bitbucket.org/weililab/scmageck/downloads/RRA_0.5.9.zip
    ###   unzip RRA_0.5.9.zip
    ###   cd RRA_0.5.9
    ###   make
    RRAPATH <- "/Library/RRA_0.5.9/bin/RRA"
    
    target_gene <- "MKI67"
    
    rra_result <- scmageck_rra(BARCODE=BARCODE, RDS=RDS, GENE=target_gene, 
                               RRAPATH=RRAPATH, LABEL='dox_mki67', 
                               NEGCTRL=NULL, KEEPTMP=FALSE, 
                               PATHWAY=FALSE, SAVEPATH=NULL)
    head(rra_result)
    
    lr_result <- scmageck_lr(BARCODE=BARCODE, RDS=RDS, LABEL='dox_scmageck_lr', 
            NEGCTRL = 'NonTargetingControlGuideForHuman', PERMUTATION = 1000,
            SAVEPATH=NULL, LAMBDA=0.01)
    lr_score <- lr_result[1]
    lr_score_pval <- lr_result[2]
    head(lr_score_pval)

scMAGeCK documentation built on Nov. 8, 2020, 7:49 p.m.