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ISAnalytics

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.

https://github.com/calabrialab/isanalytics

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.6%) to scientific vocabulary

Keywords from Contributors

grna-sequence immune-repertoire gene bioconductor-packages genomics sequencing ontologies proteomics next-generation-sequencing samtools
Last synced: 10 months ago · JSON representation

Repository

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.

Basic Info
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 1
  • Open Issues: 3
  • Releases: 1
Created about 6 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# ISAnalytics 


[![codecov](https://codecov.io/gh/calabrialab/ISAnalytics/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/calabrialab/ISAnalytics)
[![R-CMD-check-bioc DEVEL](https://github.com/calabrialab/ISAnalytics/actions/workflows/check-bioc-devel.yml/badge.svg)](https://github.com/calabrialab/ISAnalytics/actions/workflows/check-bioc-devel.yml)
[![BioC status](http://www.bioconductor.org/shields/build/devel/bioc/ISAnalytics.svg)](http://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)


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 tracking 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.

The paper is available here https://academic.oup.com/bib/article/24/1/bbac551/6955274?login=false

# 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


  Show more

```{r child="NEWS.Rmd"}
```





# Getting help

For help please contact the maintainer of the package or open an issue on GitHub.

Owner

  • Name: A. Calabria codelab
  • Login: calabrialab
  • Kind: organization
  • Location: Milan, IT

A. Calabria Codelab

GitHub Events

Total
  • Member event: 1
  • Push event: 12
  • Pull request event: 1
  • Create event: 2
Last Year
  • Member event: 1
  • Push event: 12
  • Pull request event: 1
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 157
  • Total Committers: 7
  • Avg Commits per committer: 22.429
  • Development Distribution Score (DDS): 0.096
Past Year
  • Commits: 22
  • Committers: 4
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.227
Top Committers
Name Email Commits
Giulia Pais g****1@g****m 142
Nitesh Turaga n****a@g****m 8
J Wokaty j****y@s****u 2
J Wokaty j****y 2
pais.giulia p****a@C****l 1
Andrea Calabria 3****a 1
Giulio Spinozzi g****d@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 4
  • Total pull requests: 1
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • HenrikBengtsson (2)
  • jwokaty (1)
  • sukanka (1)
Pull Request Authors
  • HenrikBengtsson (1)
  • francescogazzo (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 7,557 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: ISAnalytics

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

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 7,557 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 19.5%
Forks count: 19.8%
Average: 24.3%
Downloads: 82.2%
Maintainers (1)
gazzo.francesco@hsr.it
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • magrittr * depends
  • BiocParallel * imports
  • Rcapture * imports
  • bslib * imports
  • data.table * imports
  • datamods * imports
  • doParallel * imports
  • dplyr * imports
  • forcats * imports
  • fs * imports
  • ggplot2 * imports
  • ggrepel * imports
  • glue * imports
  • grDevices * imports
  • lifecycle * imports
  • lubridate * imports
  • psych * imports
  • purrr * imports
  • readr * imports
  • readxl * imports
  • rlang * imports
  • shiny * imports
  • shinyWidgets * imports
  • stats * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • tools * imports
  • utils * imports
  • BiocStyle * suggests
  • DT * suggests
  • R.utils * suggests
  • RefManageR * suggests
  • circlize * suggests
  • covr * suggests
  • eulerr * suggests
  • extraDistr * suggests
  • flexdashboard * suggests
  • ggalluvial * suggests
  • gridExtra * suggests
  • gtools * suggests
  • jsonlite * suggests
  • knitr * suggests
  • openxlsx * suggests
  • pheatmap * suggests
  • plotly * suggests
  • progressr * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • scales * suggests
  • sessioninfo * suggests
  • testthat * suggests
  • vegan * suggests
  • withr * suggests
.github/workflows/check-bioc-devel.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/pkgdown-devel.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite