# Scelestial: Steiner Tree Based Single-Cell Lineage Tree Inference

## Documentation for package ‘RScelestial’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.scelestial | Internal function for running scelestial algorithm.
.synthesis | Internal function for generating synthetic single-cell data through simulation of tumor growth and evolution.
as.mutation.matrix | Conversion of ten-state sequencing matrix to 0/1-mutation matrix.
as.ten.state.matrix | Conversion of 0/1 matrix to 10-state matrix
as.ten.state.matrix.from.node.seq | Generates 10-state sequence matrix from name/10-char string matrix.
distance.matrix.scelestial | Calculates distance matrix for result of scelestial
distance.matrix.tree | Calculates distance matrix for a nodes on a tree.
distance.matrix.true.tree | Calculates distance matrix for a synthetized data
Li | Bladder invasive single cell tumor dataset
my.dfs | Runs DFS on tree and calculates parent of each node as well as depth and upper-depth of nodes.
my.general.dfs | Running depth first search on a tree and calling functions on entrance/exit events
read.sequence.table | Read mutation table
RScelestial | RScelestial: An R wrapper for scelestial algorithm for single-cell lineage tree reconstruction through an approximation algorithm based on Steiner tree problem
scelestial | Infer the single-cell phylogenetic tree
synthesis | Synthesize single-cell data through tumor simulation
tree.plot | Plotting the tree