RScelestial (version 1.0.4)

Scelestial: Steiner Tree Based Single-Cell Lineage Tree Inference

Description

Scelestial infers a lineage tree from single-cell DNA mutation matrix. It generates a tree with approximately maximum parsimony through a Steiner tree approximation algorithm.

Copy Link

Version

Install

install.packages('RScelestial')

Monthly Downloads

243

Version

1.0.4

License

GPL (>= 2)

Maintainer

Mohammad Hadi Foroughmand Araabi

Last Published

November 30th, 2023

Functions in RScelestial (1.0.4)

distance.matrix.scelestial

Calculates distance matrix for result of scelestial

Bladder invasive single cell tumor dataset

as.ten.state.matrix.from.node.seq

Generates 10-state sequence matrix from name/10-char string matrix.

as.mutation.matrix

Conversion of ten-state sequencing matrix to 0/1-mutation matrix.

distance.matrix.true.tree

Calculates distance matrix for a synthetized data

.scelestial

Internal function for running scelestial algorithm.

.synthesis

Internal function for generating synthetic single-cell data through simulation of tumor growth and evolution.

as.ten.state.matrix

Conversion of 0/1 matrix to 10-state matrix

RScelestial

RScelestial: An R wrapper for scelestial algorithm for single-cell lineage tree reconstruction through an approximation algorithm based on Steiner tree problem

distance.matrix.tree

Calculates distance matrix for a nodes on a tree.

synthesis

Synthesize single-cell data through tumor simulation

Infer the single-cell phylogenetic tree

my.general.dfs

Running depth first search on a tree and calling functions on entrance/exit events

my.dfs

Runs DFS on tree and calculates parent of each node as well as depth and upper-depth of nodes.