recipe bioconductor-isanalytics

Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ISAnalytics.html

License:

CC BY 4.0

Recipe:

/bioconductor-isanalytics/meta.yaml

In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.

package bioconductor-isanalytics

versions:

1.12.0-0,  1.10.1-0,  1.8.0-0,  1.4.1-0,  1.2.0-0,  1.0.0-1

depends r-base:

>=4.3,<4.4.0a0

depends r-bslib:

depends r-datamods:

depends r-dplyr:

depends r-dt:

depends r-forcats:

depends r-fs:

depends r-ggplot2:

depends r-ggrepel:

depends r-glue:

depends r-lifecycle:

depends r-lubridate:

depends r-purrr:

depends r-readr:

depends r-readxl:

depends r-rlang:

depends r-shiny:

depends r-shinywidgets:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

requirements:

additional platforms:

Installation

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-isanalytics

and update with::

   mamba update bioconductor-isanalytics

To create a new environment, run:

mamba create --name myenvname bioconductor-isanalytics

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 quay.io/biocontainers/bioconductor-isanalytics:<tag>

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

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