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>

Citation (from within R, enter citation("LinTInd")):


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

if (!require("BiocManager", quietly = TRUE))


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


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



HTML R Script LinTInd - tutorial
PDF   Reference Manual
Text   NEWS


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
Suggests knitr, rmarkdown
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 (64-bit only)
macOS Binary (x86_64) LinTInd_1.2.0.tgz
macOS Binary (arm64) LinTInd_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: