Package: LinTInd
Title: Lineage tracing by indels
Version: 1.2.0
Authors@R: 
	c(person(given = "Luyue",family = "Wang",role = c("aut","cre"),email = "wly1995310@gmail.com"),
	person(given = "Bin",family = "Xiang",role = c("ctb")),
	person(given = "Hengxin",family = "Liu",role = c("ctb")),
	person(given = "Wu",family = "Wei",role = c("ths")))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
biocViews: SingleCell, CRISPR, Alignment
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
git_url: https://git.bioconductor.org/packages/LinTInd
git_branch: RELEASE_3_16
git_last_commit: d004cad
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: no
Packaged: 2022-11-02 01:08:00 UTC; biocbuild
Author: Luyue Wang [aut, cre],
  Bin Xiang [ctb],
  Hengxin Liu [ctb],
  Wu Wei [ths]
Maintainer: Luyue Wang <wly1995310@gmail.com>
Built: R 4.2.1; ; 2022-11-02 13:49:31 UTC; windows
