restructure repo

.gitignore

@@ -10,9 +10,14 @@ Rcode/Rprofile
 experiments/.snakemake/*
 .Rapp.history
 *.Rhistory
-experiments/data/markdowns/
-!experiments/data/markdowns/*topSeparators.Rmd
-experiments/data/htmls/*files
-experiments/logs/
+experiments/assessing_cluster_clonality/data/markdowns/
+!experiments/assessing_cluster_clonality/data/markdowns/*topSeparators.Rmd
+experiments/assessing_cluster_clonality/data/htmls/*files
+experiments/assessing_cluster_clonality/logs/
+experiments/assessing_cluster_clonality/workflow/scripts/CTC_parseSampling/testData
+experiments/assessing_cluster_clonality/data/htmls/*
 *.vscode
 *ipynb*
+*.RProj
+*lsf*
+*slurm*

README.md

@@ -1,3 +1,30 @@
 [![Super-Linter](https://github.com/JohannesGawron/CTC-SCITE/actions/workflows/linter.yml/badge.svg)](https://github.com/marketplace/actions/super-linter)
-[![Snakemake](https://img.shields.io/badge/snakemake-≥8.0-brightgreen.svg)](https://snakemake.github.io) 
-[![Code style: snakefmt](https://img.shields.io/badge/code%20style-snakefmt-000000.svg)](https://github.com/snakemake/snakefmt)
+
+
+
+# Interrogating the clonality of circulating tumor cell (CTC) clusters
+========
+
+This repository accompanies the publication doi....
+
+## Synopsis
+-----------
+
+
+The clonal diversity of cells within individual CTC clusters in human malignancies is poorly defined. In this study, we provide substantial evidence for the presence and quantification of the prevalence of oligoclonal CTC clusters in human cancer.
+
+
+## Contents
+-----------
+
+
+*  CTC_SCITE: It contains the CTC-SCITE algorithm, a bayesian phylogenetic tree inference algorithm which takes the genomic profiles of circulating tumor cells and ciculating tumor cell clusters and infers a phylogenetic tree on all cells, jointly calling the genotypes of each cell
+
+*  Experiments: Analyses of CTCs and CTC clusters from breast, prostate, lung, and ovarian cancer patients, as well as from mouse cancer models. We infer the clonality of CTC clusters, and quantitatively study the prevalence of oligoclonal CTC clusters as a function of the clonal complexity of primary tumors, based on a injection of genetically barcoded xenografts into mice.
+
+
+## Availability
+-----------
+
+
+All software is freely available under a GPL3 license.