scDAPA-demo

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
if (!require("rtracklayer")) BiocManager::install("rtracklayer")

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if (!require("ggplot2")) install.packages("ggplot2")

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if (!require("ggbio")) BiocManager::install("ggbio")

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if (!require("stringr")) install.packages("stringr")

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if (!require("tools")) install.packages("tools")

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install.packages("/Users/ozlemtuna/Downloads/scDAPA/scDAPAminer_1.1.tar.gz",repos = NULL, type = "source")

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library(scDAPAminer)
input_file1 <- system.file("extdata", "MG0.anno", package = "scDAPAminer")
input_file2 <- system.file("extdata", "sMG3.anno", package = "scDAPAminer")
scDAPAdetect(file1=input_file1,file2=input_file2,type='f2f',output_dir='./',bin_size=100,count_cutoff=20)

## [1] "type f2f"
## [1] "perform MG0 vs. sMG3 comparision..."

input_file1 <- system.file("extdata", "MG0.anno", package = "scDAPAminer")
input_file2 <- system.file("extdata", "sMG3.anno", package = "scDAPAminer")
# download Mus_musculus.GRCm38.84.gtf from Ensembl.
gtf=import('/Users/ozlemtuna/Downloads/scDAPA/Mus_musculus.GRCm38.84.gtf')
dp = scDAPAview(files=c(input_file1,input_file2),alt_names=c('MG0','sMG3'),gtf=gtf,gene_id='ENSMUSG00000073490')

## Constructing graphics...

dp

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