LinTInd
This is the development version of LinTInd; for the stable release version, see LinTInd.
Lineage tracing by indels
Bioconductor version: Development (3.21)
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("LinTInd")):
Installation
To install this package, start R (version "4.5") 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")| LinTInd - tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, CRISPR, SingleCell, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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, pwalign, 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | LinTInd_1.11.0.zip (64-bit only) |
| macOS Binary (x86_64) | LinTInd_1.11.0.tgz |
| macOS Binary (arm64) | LinTInd_1.11.0.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 |