m6A-express is a tool to identify m6A methylation significantly regulated expression genes in specific context
Before installing m6A-express package, user should have installed python 2.7 software in their platform (Windows systerm or Linux systerm). And some python packages should be installed, such as numpy, statsmodels.api, pandas, scipy.
The m6A-express package can be installed by the following R commands:
devtools::install_github("tengzhang123/m6A-express")
library(m6A-express)
The following command code will show how to use this package and output m6A methylation regulated expression gene in excel files
f1 <- system.file("extdata", "IP1.bam", package="m6A-express")
f2 <- system.file("extdata", "IP2.bam", package="m6A-express")
f3 <- system.file("extdata", "IP3.bam", package="m6A-express")
f4 <- system.file("extdata", "IP4.bam", package="m6A-express")
f5 <- system.file("extdata", "Input1.bam", package="m6A-express")
f6 <- system.file("extdata", "Input2.bam", package="m6A-express")
f7 <- system.file("extdata", "Input3.bam", package="m6A-express")
f8 <- system.file("extdata", "Input4.bam", package="m6A-express")
IP_BAM <- c(f1,f2,f3,f4)
INPUT_BAM <- c(f5,f6,f7,f8)
gtf <- system.file("extdata", "hg19toy.gtf", package="m6A-express")
m6A_reg_exp_gene <- m6A_express(express_data=INPUT_BAM, IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM, annot_type="hg19", GENE_ANNO_GTF=gtf, pvalue=0.05,mode="basic")
IP_BAM <- c(f1,f2)
TREATED_IP_BAM <- c(f3,f4)
INPUT_BAM <- c(f5,f6)
TREATED_INPUT_BAM <- c(f7,f8)
m6A_reg_exp_gene <- m6A_express(express_data=INPUT_BAM, treated_express_data=TREATED_INPUT_BAM, IP_BAM=IP_BAM, TREATED_IP_BAM=TREATED_IP_BAM, INPUT_BAM=INPUT_BAM, TREATED_INPUT_BAM=TREATED_INPUT_BAM,annot_type="hg19", GENE_ANNO_GTF=gtf,pvalue=0.05,mode="DE-DM")
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