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# ISAnalytics <a href='https://bioconductor.org/packages/3.12/bioc/html/ISAnalytics.html'><img src='man/figures/logo.png' align="right" height="250" /></a>
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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.
# Installation
## Installation from bioconductor
RELEASE version:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ISAnalytics")
```
DEVEL version:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ISAnalytics")
```
## Installation from GitHub
IMPORTANT NOTE: as of today the package `knitcitations` which is used in
our vignettes, is temporarily unavailable through CRAN and can lead to
the failure of package installation. This issue should be solved in the
near future, in the meantime please use the safer option (you have to
install suggested dependencies manually).
RELEASE:
``` r
if (!require(devtools)) {
install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
ref = "RELEASE_3_12",
dependencies = TRUE,
build_vignettes = TRUE)
## Safer option for vignette building issue
devtools::install_github("calabrialab/ISAnalytics",
ref = "RELEASE_3_12")
```
DEVEL:
``` r
if (!require(devtools)) {
install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
ref = "master",
dependencies = TRUE,
build_vignettes = TRUE)
## Safer option for vignette building issue
devtools::install_github("calabrialab/ISAnalytics",
ref = "master")
```
# Visit the package website
You can visit the package website to view documentation, vignettes and
more at this link: [ISAnalytics
Website](https://calabrialab.github.io/ISAnalytics/)
# Current functionality
- Import integration matrices from files: more info with
`vignette("How to use import functions", package = "ISAnalytics")`
- Collision removal: more info with `vignette("Collision removal
functionality", package = "ISAnalytics")`
- Aggregation: more info with `vignette("Working with aggregate
functions", package = "ISAnalytics")`
- Re-calibration functions: `compute_near_integrations`
- Analysis functions: `compute_abundance`, `comparison_matrix`
`separate_quant_matrices`, others
- Plotting functions: `CIS_volcano_plot`
- Utility functions
# NEWS
# ISAnalytics 1.1.3 (2020-11-10)
## FIXES
- Further fixes for printing reports when widgets not available
- Added progress bar to collision processing in `remove_collisions`
- Updated vignettes
## NEW
- Added vignette “Using ISAnalytics without RStudio support”
# ISAnalytics 1.1.2 (2020-11-05)
## FIXES
- Fixed missing restarts for non-blocking widgets
# ISAnalytics 1.1.1 (2020-11-04)
## FIXES
- Functions that make use of widgets do not interrupt execution
anymore if errors are thrown while producing or printing the widgets
- Optimized widget printing for importing functions
- If widgets can’t be printed and verbose option is active, reports
are now displayed on console instead (needed for usage in
environments that do not have access to a browser)
- Other minor fixes (typos)
- Bug fixes: fixed a few bugs in importing and recalibration functions
- Minor fix in import\_association\_file file function: added multiple
strings to be translated as NA
## IMPORTANT NOTES
- Vignette building might fail due to the fact that package
“knitcitations” is temporarily unavailable through CRAN
- ISAnalytics is finally in release on bioconductor\!
# ISAnalytics 0.99.14 (2020-10-21)
- Minor fixes in tests
# ISAnalytics 0.99.13 (2020-10-19)
## NEW FEATURES
- Added analysis functions `CIS_grubbs` and `cumulative_count_union`
- Added plotting functions `CIS_volcano_plot`
# ISAnalytics 0.99.12 (2020-10-04)
## NEW FEATURES
- Added analysis function `sample_statistics`
## SIGNIFICANT USER-VISIBLE CHANGES
- `aggregate_values_by_key` has a simplified interface and supports
multi-quantification matrices
## MINOR CHANGES
- Updated vignettes
- `import_parallel_Vispa2Matrices_interactive` and
`import_parallel_Vispa2Matrices_auto` now have an option to return a
multi-quantification matrix directly after import instead of a list
# ISAnalytics 0.99.11 (2020-09-21)
## NEW FEATURES
- Added analysis functions `threshold_filter`, `top_integrations`
- Added support for multi-quantification matrices in
`compute_abundance`
## MINOR FIXES
- Fixed bug in `comparison_matrix` that ignored custom column names
- Fixed issues in some documentation pages
# ISAnalytics 0.99.10 (2020-09-14)
ISanalytics is officially on bioconductor\!
## NEW FEATURES
- Added analysis functions `comparison_matrix` and
`separate_quant_matrices`
- Added utility function `as_sparse_matrix`
- Added package logo
## SIGNIFICANT USER-VISIBLE CHANGES
- Changed algorithm for `compute_near_integrations`
- Added support for multi-quantification matrices to
`remove_collisions`
- Added usage of lifecycle badges in documentation: users can now see
if a feature is experimental/maturing/stable etc
## MINOR FIXES
- Added fix for `import_single_Vispa2Matrix` to remove non significant
0 values
# ISAnalytics 0.99.9 (2020-09-01)
## NEW FEATURES
- Added functionality: aggregate functions
- Added vignette on aggregate functions
- Added recalibration functions
- Added first analysis function (compute\_abundance)
## SIGNIFICANT USER-VISIBLE CHANGES
- Dropped structure `ISADataFrame`: now the package only uses standard
tibbles
- Modified package documentation
# ISAnalytics 0.99.8 (2020-08-12)
- Submitted to Bioconductor
# TO DO in future updates
- [ ] Add vignette for association file usage
- [ ] Add vignette for re-calibration functionality
- [x] Add support for multi-quantification matrices to several
functions (ISAnalytics 0.99.12)
# Getting help
For help please contact the maintainer of the package or open an issue
on GitHub.
