recipe bioconductor-lintind

Lineage tracing by indels






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.

package bioconductor-lintind

(downloads) docker_bioconductor-lintind



depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-ggtree:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends r-ape:

depends r-base:


depends r-cowplot:

depends r-data.tree:

depends r-dplyr:

depends r-ggnewscale:

depends r-ggplot2:

depends r-networkd3:

depends r-pheatmap:

depends r-purrr:

depends r-reshape2:

depends r-rlist:

depends r-stringdist:

depends r-stringr:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-lintind

and update with::

   mamba update bioconductor-lintind

To create a new environment, run:

mamba create --name myenvname bioconductor-lintind

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-lintind/tags`_ for valid values for ``<tag>``)

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