Package: RScelestial 1.0.4

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

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.

Authors:Mohammad Hadi Foroughmand Araabi [aut, cre], Sama Goliaei [aut, ctb], Alice McHardy [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RScelestial/json (API)

# Install 'RScelestial' in R:

install.packages('RScelestial', repos = c('https://foroughmand.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

Li - Bladder invasive single cell tumor dataset

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.00 score 3 scripts 276 downloads 14 exports 1 dependencies

Last updated from:cdb757ecd6. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	316
linux-devel-x86_64	OK	137
source / vignettes	OK	358
linux-release-arm64	OK	138
linux-release-x86_64	OK	144
macos-release-arm64	OK	169
macos-release-x86_64	OK	314
macos-oldrel-arm64	OK	239
macos-oldrel-x86_64	OK	289
windows-devel	OK	99
windows-release	OK	103
windows-oldrel	OK	126
wasm-release	OK	144

Exports:.scelestial .synthesis as.mutation.matrix as.ten.state.matrix as.ten.state.matrix.from.node.seq distance.matrix.scelestial distance.matrix.tree distance.matrix.true.tree my.dfs my.general.dfs read.sequence.table scelestial synthesis tree.plot

Dependencies:Rcpp

RScelestial Vignette

Installing RScelestial | Simulation | Inferring the phylogenetic tree | Evaluating results | Running Scelestial on multiple sequence alignment

Rendered fromRScelestial-vignette.Rmdusingknitr::rmarkdown

Last update: 2023-12-01
Started: 2019-11-28

Citation

Readme and manuals

Help Manual

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

Package: RScelestial 1.0.4

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)