The eccDNAscopeR package currently only supports Linux systems and requires a complex software environment. We strongly recommend users to run it within a conda environment.

1.Creat conda environment

conda create -n  eccDNAscope python=3.7 r-base=4.3.2 # It is recommended to use Python 3.7 and R 4.3.2 versions.
conda activate eccDNAscope

2.Configure the software environment

# Install R packages
conda install -y bioconda::bioconductor-genomicranges # 1.54.1
conda install -y r-ggplot2=3.4.4
conda install -y r-seurat=4.3.0 # eccDNAscope was built with Seurat v4
conda install -y r-signac=1.14.0
conda install -y bioconda::bioconductor-chipseeker # 1.38.0
conda install -y bioconda::bioconductor-org.hs.eg.db # 3.18.0
conda install -y bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene # 3.18.0
conda install -y bioconda::bioconductor-genesummary # 0.99.6
conda install -y bioconda::bioconductor-omiccircos # 1.40.0

# Install python packages
conda install -y numpy=1.19.5 pandas=1.3.5 scipy=1.7.3 statsmodels=0.13.2

# Install java8
conda install -y openjdk=8

# other packages
conda install -y samtools bedtools

3.Install eccDNAscope in R

Click here to download the eccDNAscope R package 

# You can then install eccDNAscope on your system using the following method.
install.packages("eccDNAscope_example/eccDNAscope_0.1.0.tar.gz", 
                 repos=NULL, type="source")