ISAnalytics
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ISAnalytics.
Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
Bioconductor version: 3.14
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: Andrea Calabria [aut, cre], Giulio Spinozzi [aut], Giulia Pais [aut]
Maintainer: Andrea Calabria <calabria.andrea at hsr.it>
citation("ISAnalytics")):
Installation
To install this package, start R (version "4.1") 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")| aggregate_function_usage | HTML | R Script |
| collision_removal | HTML | R Script |
| import_functions_howto | HTML | R Script |
| sharing_analyses | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Sequencing, SingleCell, Software |
| Version | 1.4.3 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | CC BY 4.0 |
| Depends | R (>= 4.1), magrittr |
| Imports | utils, dplyr, readr, tidyr, purrr, rlang, tibble, BiocParallel, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, psych, data.table, readxl, tools, Rcapture, grDevices, zip |
| System Requirements | |
| URL | https://calabrialab.github.io/ISAnalytics https://github.com//calabrialab/isanalytics |
| Bug Reports | https://github.com/calabrialab/ISAnalytics/issues |
See More
| Suggests | testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, DT, circlize, plotly, gtools, eulerr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ISAnalytics_1.4.3.tar.gz |
| Windows Binary | ISAnalytics_1.4.3.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | ISAnalytics_1.4.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ISAnalytics |
| Source Repository (Developer Access) | git clone [email protected]:packages/ISAnalytics |
| Bioc Package Browser | https://code.bioconductor.org/browse/ISAnalytics/ |
| Package Short Url | https://bioconductor.org/packages/ISAnalytics/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |