LinTInd

DOI: 10.18129/B9.bioc.LinTInd  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see LinTInd.

Lineage tracing by indels

Bioconductor version: 3.16

When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagProcess() function will help you to extract indels for each cell or read. TagDist() function will help you to calculate the similarity between each pair of groups across the indwells they contain. BuildTree() function will help you to reconstruct a tree. PlotTree() function will help you to visualize the tree.

Author: Luyue Wang [aut, cre], Bin Xiang [ctb], Hengxin Liu [ctb], Wu Wei [ths]

Maintainer: Luyue Wang <wly1995310 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("LinTInd")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("LinTInd")

 

HTML	R Script	LinTInd - tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, CRISPR, SingleCell, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.0), ggplot2, parallel, stats, S4Vectors
Imports	data.tree, reshape2, networkD3, stringdist, purrr, ape, cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap, Biostrings, IRanges, BiocGenerics(>= 0.36.1), ggtree
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	LinTInd_1.2.0.tar.gz
Windows Binary	LinTInd_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	LinTInd_1.2.0.tgz
macOS Binary (arm64)	LinTInd_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LinTInd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LinTInd
Bioc Package Browser	https://code.bioconductor.org/browse/LinTInd/
Package Short Url	https://bioconductor.org/packages/LinTInd/
Package Downloads Report	Download Stats