Update README.md

README.md

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-# single_cell_lung_adenocarcinoma
+# Single-cell RNA sequencing
+Here you find complementary code used for our paper "Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma".
+The main code used to generate the main figures can be found here: https://codeocean.com/capsule/0121060/tree.
+
+## inferCNV
+1) Run the preprocessing and cell type annotation steps as described here: https://codeocean.com/capsule/0121060/tree.
+2) Use the seurat object epi_anno and apply the inferCNV algorithm as described in infercnv_nsclc.R
+3) Proceed with further epithelial analyses as described here: https://codeocean.com/capsule/0121060/tree.
+
+## Validation using the dataset from Kim et al. 2020
+1) Gene expression and clinical data can be downloaded here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131907.
+2) Data was preprocessed as described here: lung_kim_et_al_preprocessing.Rmd
+3) Cell type labels were transfered from our dataset to the Kim et al. dataset as described here: lung_ingest.ipynb
+4) For further analyses of stromal and immune cells and correlation analyses of different cell types, see: https://codeocean.com/capsule/0121060/tree.