Update README.md

SCENIC_CART/README.md

@@ -7,3 +7,15 @@ In details, starting from the UMI count matrix, the potential targets of the sam
 - SCENIC_CART_HM.R: R script to produce the heatmap on the results of the SCENIC analysis.
 
 ![Full_CART_HM](./Full_CART_HM.png)
+
+---
+
+#### SCENIC Analyis ####
+
+1. Convert Seurat object into _loom_: `Rscript export_loom.R <Full_CART.rds> <Full_CART.loom>`
+
+2. Gene regulatory network inference: `pyscenic grn --num_workers 8 -output <Full_CART.adjacences.tsv> --method grnboost2 <Full_CART.loom> mm_tfs.txt`
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+3. Regulon prediction: `pyscenic ctx --annotations_fname motifs-v9-nr.mgi-m0.001-o0.0.tbl --expression_mtx_fname <Full_CART.loom> --mode 'dask_multiprocessing' --num_workers 8 --output <Full_CART.regulons.tsv> <Full_CART.adjacences.tsv> mm9-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather mm9-tss-centered-5kb-10species.mc9nr.genes_vs_motifs.rankings.feather mm9-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather`
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+4. Cellular enrichment: `pyscenic aucell --num_workers 8 --output <Full_CART.from_tsv.loom> <Full_CART.loom> <Full_CART.regulons.tsv>`