Set up conda environment

conda install r-essentials
conda install conda-forge::r-hdf5r
conda install r-devtools
conda install bioconda::bioconductor-dirichletmultinomial
conda install bioconda::bioconductor-chromvar
conda install bioconda::bioconductor-scran
conda install bioconda::bioconductor-infercnv
conda install bioconda::macs2
conda install samtools
conda install conda-forge::r-rstatix
conda install conda-forge::cairo

Install SCENIC+ in the same conda environment

git clone https://github.com/aertslab/scenicplus cd scenicplus pip install -e .

In R install:

install.packages("BiocManager")
install.packages("paletteer")
setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies install.packages ("Signac")
install.packages ('remotes'). remotes::install_github("stuart-lab/signac", ref="develop"). install.packages ('Seurat')
devtools::install_github("crazyhottommy/scATACutils")
BiocManager::install ('ComplexHeatmap')
BiocManager::install ('regioneR')
BiocManager::instlall ('BSgenome.Hsapiens.UCSC.hg38')
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
BiocManager::install ('TxDb.Hsapiens.UCSC.hg38.knownGene') install.packages(c("ggdendro"))
BiocManager::install(c("GenomicAlignments", "plyranges", "Rsamtools", "GenomeInfoDb", "BSgenome.Hsapiens.UCSC.hg38", "GenomicRanges", "Biostrings", "BiocGenerics", "S4Vectors", "GenomicFeatures"))
devtools::install_github("colomemaria/epiAneufinder")
devtools::install_github('immunogenomics/presto')
devtools::install_github("GreenleafLab/chromVARmotifs")
BiocManager::install("fgsea")
BiocManager::install("clusterProfiler")
BiocManager::install(c("WGCNA", "igraph", "devtools", "GeneOverlap", "ggrepel", "UCell")) install.packages ('ape') install.packages('dendextend') conda install conda-forge::r-factoextra BiocManager::install ('org.Hs.eg.db') install.packages ('RColorBrewer')
install.packages ('survminer') #devtools::install_github("ricardo-bion/ggradar") BiocManager::install("RTCGA") BiocManager::install("liftOver")
install.packages("scCustomize")
install.packages("ggpubr")
BiocManager::install("liftOver") install.packages ('GSA') devtools::install_github("GreenleafLab/chromVARmotifs") BiocManager::install("compEpiTools") install.packages("harmony")
install.packages("zoo") devtools::install_github('smorabit/hdWGCNA', ref='dev')

Run cNMF scripts on LSF batch submission

Scripts to run cNMF are in utils and include:
cnmf_prepare_inputs.R
cnmf_master.sh
cnmf_factorization_parallel.sh
cnmf_format_spectra_files.R

Run cNMF

nfeat = 5000 # specify number of features to use
force=F # force re-running when output already present
k_list = c(5:30) # number of K to compute
k_selections = c(5:30) # number of K to compute
cores= 100 # specify number of cores for array job
cnmf_name = 'CD8_exhausted' # specify name of cnmf run
cnmf_out = path/to/output # path to cnmf output
git_repo = path/to/git_repo # path to git repo

RUN consensus NMF from R

source (file.path ('git_repo','utils','cnmf_prepare_inputs.R')) # source cNMF to prepare count matrices and run cnmf algorithm

Import and format spectra files in R

k_selection = 30 # select a K after examining error / performance cNMF plot source (file.path ('git_repo','utils','cnmf_format_spectra_files.R'))

Install conda env for averaging h5 files from chromBPnet

conda create -n h5py python=3.8 conda install conda-forge/label/cf202003::hdf5plugin conda install bioconda::wiggletools conda install bioconda::ucsc-wigtobigwig