ISAnalytics
This is the released version of ISAnalytics; for the devel version, see ISAnalytics.
Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
Bioconductor version: Release (3.23)
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.
Author: Francesco Gazzo [cre] 
, Giulia Pais [aut] , Andrea Calabria [aut], Giulio Spinozzi [aut]
Maintainer: Francesco Gazzo <gazzo.francesco at hsr.it>
citation("ISAnalytics")):Giulia Pais, Andrea Calabria, Giulio Spinozzi. ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies. doi:10.18129/B9.bioc.ISAnalytics, R package version 1.22.0, https://bioconductor.org/packages/ISAnalytics.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ISAnalytics")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("ISAnalytics")| ISAnalytics | HTML | R Script |
| workflow_start | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, DataImport, FunctionalGenomics, Sequencing, SingleCell, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | CC BY 4.0 |
| Depends | R (>= 4.5) |
| Imports | utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, vegan, data.table, DT |
| System Requirements | |
| URL | https://calabrialab.github.io/ISAnalytics https://github.com//calabrialab/isanalytics https://calabrialab.github.io/ISAnalytics/ |
| Bug Reports | https://github.com/calabrialab/ISAnalytics/issues |
See More
| Suggests | testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, Rcapture |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ISAnalytics_1.22.0.tar.gz |
| Windows Binary (x86_64) | ISAnalytics_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | ISAnalytics_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | ISAnalytics_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ISAnalytics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ISAnalytics |
| Package Short Url | https://bioconductor.org/packages/ISAnalytics/ |
| Package Downloads Report | Download Stats |