First, conda environment needs to be created.
conda env create -f cell2cell_workshop_env.yml
Download required files.
wget https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5
wget https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz
wget https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz.tbi
wget https://atlas.fredhutch.org/data/nygc/multimodal/pbmc_multimodal.h5seurat
wget https://ftp.ensembl.org/pub/release-108/gtf/homo_sapiens/Homo_sapiens.GRCh38.108.chr.gtf.gz
gunzip Homo_sapiens.GRCh38.108.chr.gtf.gz
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz
curl -o pbmc_network.rds -L 'https://drive.google.com/uc?export=download&confirm=yes&id=1jWZAA2l6ePa4JtFv2eViwCmSgINI72Lk'
curl -o transfer.anchors.rds -L 'https://drive.google.com/uc?export=download&confirm=yes&id=1Y8TufsX4A6NynBksrLPJ0Mgvs1Y6dBrr'
Download required tool.
wget https://meme-suite.org/meme/meme-software/5.5.0/meme-5.5.0.tar.gz
tar -xf meme-5.5.0.tar.gz
cd meme-5.5.0
./configure --enable-build-libxml2 --enable-build-libxslt
make
make install
Activate the environment.
conda activate cell2cell_workshop_env
Start a new R session by typing R and download required packages.
install.packages(c("BiocManager", "remotes", "qlcMatrix", "ggforce", "assertthat"))
BiocManager::install(c("Signac", "EnsDb.Hsapiens.v86", "BSgenome.Hsapiens.UCSC.hg38",
"biovizBase", "RcisTarget", "org.Hs.eg.db",
"TxDb.Hsapiens.UCSC.hg38.knownGene", "RCy3"))
remotes::install_github("mojaveazure/seurat-disk")
remotes::install_github("satijalab/seurat-data")
remotes::install_github("jiang-junyao/IReNA")
remotes::install_github('satijalab/seurat-wrappers')For peak calling, Macs2 path needs to be specified. It can be found by
typing which macs2.