Name Mode Size
..
ISAnalytics-deprecated.R 100644 1 kb
ISAnalytics-package.R 100644 2 kb
aggregate-functions.R 100644 10 kb
analysis-functions.R 100644 67 kb
collision-removal.R 100644 12 kb
data.R 100644 3 kb
exported-vars.R 100644 20 kb
import-functions.R 100644 43 kb
internal-functions.R 100644 234 kb
internal-msgs.R 100644 16 kb
outlier-filtering.R 100644 18 kb
plotting-functions.R 100644 74 kb
population-size-estimate.R 100644 16 kb
purity-filter.R 100644 10 kb
recalibration-functions.R 100644 14 kb
report-utilities.R 100644 4 kb
server.R 100644 12 kb
ui.R 100644 2 kb
utility-functions.R 100644 44 kb
zzz.R 100644 0 kb
README.Rmd
--- output: github_document --- <!-- README.md is generated from README.Rmd. Please edit that file --> ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" ) ``` # ISAnalytics <a href='https://bioconductor.org/packages/3.12/bioc/html/ISAnalytics.html'><img src='man/figures/logo.png' align="right" height="250" /></a> <!-- badges: start --> [![codecov](https://codecov.io/gh/calabrialab/ISAnalytics/branch/master/graph/badge.svg)](https://codecov.io/gh/calabrialab/ISAnalytics) [![R build status - bioc](https://github.com/calabrialab/isanalytics/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/calabrialab/isanalytics/actions) [![BioC status](http://www.bioconductor.org/shields/build/devel/bioc/ISAnalytics.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) <!-- badges: end --> ISAnalytics is an R package developed to analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies. 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. # Visit the package website You can visit the package website to view documentation, vignettes and more. * For the release version: [ISAnalytics Website release](https://calabrialab.github.io/ISAnalytics/) * For the devel version: [ISAnalytics Website dev](https://calabrialab.github.io/ISAnalytics/dev) ```{r child="inst/rmd/install_and_options.Rmd"} ``` # NEWS <details> <summary>Show more</summary> ```{r child="NEWS.Rmd"} ``` </details> # Getting help For help please contact the maintainer of the package or open an issue on GitHub.