- 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:
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:
1.20.1-0,1.12.0-0,1.10.1-0,1.8.0-0,1.4.1-0,1.2.0-0,1.0.0-1- Depends:
on r-base
>=4.5,<4.6.0a0on r-bslib
on r-data.table
on r-datamods
on r-dplyr
on r-dt
on r-forcats
on r-fs
on r-ggplot2
on r-ggrepel
on r-glue
on r-lifecycle
on r-lubridate
on r-purrr
on r-readr
on r-readxl
on r-rlang
on r-shiny
on r-shinywidgets
on r-stringr
on r-tibble
on r-tidyr
on r-vegan
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-isanalytics
to add into an existing workspace instead, run:
pixi add bioconductor-isanalytics
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-isanalytics
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-isanalytics
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-isanalytics:<tag>
(see bioconductor-isanalytics/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-isanalytics/README.html)
