LinTInd

DOI: 10.18129/B9.bioc.LinTInd    

This is the development version of LinTInd; for the stable release version, see LinTInd.

Lineage tracing by indels

Bioconductor version: Development (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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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Details

biocViews Alignment, CRISPR, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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
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Build Report  

Package Archives

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

Source Package LinTInd_1.1.0.tar.gz
Windows Binary LinTInd_1.1.0.zip
macOS 10.13 (High Sierra) LinTInd_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/LinTInd
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/LinTInd
Package Short Url https://bioconductor.org/packages/LinTInd/
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