Welcome to the new bioconductor.org!

LinTInd

Lineage tracing by indels


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
LinTInd - tutorial HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, CRISPR, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
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
System Requirements
URL
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package LinTInd_1.6.0.tar.gz
Windows Binary LinTInd_1.6.0.zip
macOS Binary (x86_64) LinTInd_1.6.0.tgz
macOS Binary (arm64) LinTInd_1.6.0.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