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<!-- is generated from README.Rmd. Please edit that file --> # ISAnalytics <a href=''><img src='man/figures/logo.png' align="right" height="250" /></a> <!-- badges: start --> [![codecov](]( [![R-CMD-check-bioc RELEASE](]( [![Lifecycle: stable](]( [![Bioc release status](]( <!-- 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. The paper is available here <> # Visit the package website You can visit the package website to view documentation, vignettes and more. - For the release version: [ISAnalytics Website release]( - For the devel version: [ISAnalytics Website dev]( # Installation and options `ISAnalytics` can be installed quickly in different ways: - You can install it via [Bioconductor]( - You can install it via GitHub using the package `devtools` There are always 2 versions of the package active: - `RELEASE` is the latest stable version - `DEVEL` is the development version, it is the most up-to-date version where all new features are introduced ## 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 RELEASE: ``` r if (!require(devtools)) { install.packages("devtools") } devtools::install_github("calabrialab/ISAnalytics", ref = "RELEASE_3_16", dependencies = TRUE, build_vignettes = TRUE) ``` DEVEL: ``` r if (!require(devtools)) { install.packages("devtools") } devtools::install_github("calabrialab/ISAnalytics", ref = "master", dependencies = TRUE, build_vignettes = TRUE) ``` ## Setting options `ISAnalytics` has a verbose option that allows some functions to print additional information to the console while they’re executing. To disable this feature do: ``` r # DISABLE options("ISAnalytics.verbose" = FALSE) # ENABLE options("ISAnalytics.verbose" = TRUE) ``` Some functions also produce report in a user-friendly HTML format, to set this feature: ``` r # DISABLE HTML REPORTS options("ISAnalytics.reports" = FALSE) # ENABLE HTML REPORTS options("ISAnalytics.reports" = TRUE) ``` # NEWS <details> <summary> Show more </summary> # ISAnalytics 1.8.3 (2023-04-03) ## ENHANCES AND REFACTORING - The package no longer depends on `magrittr` - All functionality associated with `data.table` now it’s completely optional and will be used internally only if the package is available - Several packages were moved from `Imports` to `Suggests` - functions will notify when additional packages are requested for the specific functionality - All known deprecated or superseded functions from other packages have been removed or substituted ## FIXES AND GENERAL UPDATES - Added a new tag “barcode_mux” in `available_tags()` - The function `HSC_population_size_estimate()` now better supports the computation of estimates from different groups of cell types and tissues at the same time. The tabular output now contains an additional column “Timepoints_included” that specifies how many time points the estimate contains - Function `is_sharing()` can now handle better limit cases and has the option of being parallelised provided appropriate packages are available (better performance) ## DEPRECATIONS & BREAKING CHANGES - Functions `import_parallel_Vispa2Matrices_auto()` and `import_parallel_Vispa2Matrices_interactive()` are officially defunct and will not be exported anymore starting from the next release cycle - The argument `mode` of `import_parallel_Vispa2Matrices()` no longer accepts `INTERACTIVE` as a valid option and the interactive mode is considered now defunct, since the usage is very limiting and limited - The argument `association_file` of `import_parallel_Vispa2Matrices()` no longer accepts a string representing a path. Association file import is delegated solely to its dedicated function from now on. - The function `threshold_filter()` is deprecated, since its use is rather complicated instead of using standard filtering with dplyr or similar tools ## MINOR CHANGES - `default_af_transform()` now pads time points based on the maximum number of characters + 1 in the column # ISAnalytics 1.8.2 (2023-01-26) ## FIXES AND GENERAL UPDATES - Fixed an issue with ifelse function in `top_abund_tableGrob()` - now the function has a new argument `transform_by` which is useful for controlling ordering of columns - Updated CITATION file - Package `DT` has been moved (likely temporarily) in Imports - linked to issue <> - Fixed other typos and minor issues # ISAnalytics 1.8.1 (2022-12-01) - Fixed all `tidyselect` warnings (internal use of .data\$ in selection context) - Added bonferroni correction in `gene_frequency_fisher` # ISAnalytics 1.7.7 (2022-10-26) - Added new section in workflow vignette + sample files # ISAnalytics 1.7.6 (2022-10-25) - Fixed minor bugs and typos # ISAnalytics 1.7.5 (2022-10-05) - Fixed build issues # ISAnalytics 1.7.4 (2022-10-04) ## VISIBLE USER CHANGES - Progress bars for long processing functions are now implemented via the package `progressr`, added a wrapper function for fast enabling progress bars, `enable_progress_bars()` - Introduced logging for issues in `HSC_population_size_estimate()` - signals eventual problems in computing estimates and why ## BUG FIXES AND MINOR CHANGES - Fixed minor bugs and typos # ISAnalytics 1.7.3 (2022-06-17) ## BUG FIXES AND MINOR CHANGES - All functions that check for options now have a default value if option is not set - `CIS_grubbs` function is now faster (removed dependency from `psych::describe`) ## NEW - New functions `CIS_grubbs_overtime()` and associated plotting function `top_cis_overtime_heatmap()` to compute CIS_grubbs test over time # ISAnalytics 1.7.2 (2022-05-23) ## BUG FIXES AND MINOR CHANGES - Fixed minor issues in `import_association_file()` - function had minor issues when importing \*.xlsx files and missing optional columns threw errors - Fixed bug in `as_sparse_matrix()` - function failed when trying to process an aggregated matrix ## NEW - Added 2 new utility functions `export_ISA_settings()` and `import_ISA_settings()` that allow a faster workflow setup # ISAnalytics 1.7.1 (2022-05-04) ## BUG FIXES AND MINOR CHANGES - Fixed minor issue in `compute_near_integrations()` - function errored when `report_path` argument was set to `NULL` - Fixed dplyr warning in `integration_alluvial_plot()` internals - Fixed issue with report of VISPA2 stats - report failed due to minor error in rmd fragment - Internals of `remove_collisions()` use again dplyr internally for joining and grouping operations - needed because of performance issues with data.table - `fisher_scatterplot()` has 2 new arguments that allow the disabling of highlighting for some genes even if their p-value is under the threshold # ISAnalytics 1.5.4 (2022-04-20) ## MAJOR CHANGES - ISAnalytics has now a new “dynamic vars system” to allow more flexibility on user inputs, view the dedicated vignette with `vignette("workflow_start", package="ISAnalytics")` - All package functions were reviewed to work properly with this system ## NEW FEATURES - `gene_frequency_fisher()` is a new function of the analysis family that allows the computation of Fisher’s exact test p-values on gene frequency - `fisher_scatterplot()` is the associated plotting function - `top_targeted_genes()` is a new function of the analysis family that produces the top n targeted genes based on the number of IS - `NGSdataExplorer()` is a newly implemented Shiny interface that allows the exploration and plotting of data - zipped examples were removed from the package to contain size. To compensate, the new function `generate_default_folder_structure()` generates the standard folder structure with package-included data on-demand - `transform_columns()` is a new utility function, also used internally by other exported functions, that allows arbitrary transformations on data frame columns ## MINOR CHANGES - `remove_collisions()` now has a dedicated parameter to specify how independent samples are identified - `compute_near_integration_sites()` now has a parameter called `additional_agg_lambda()` to allow aggregation of additional columns - `CIS_grubbs()` now signals if there are missing genes in the refgenes table and eventually returns them as a df - `outlier_filter()` is now able to take multiple tests in input and combine them with a given logic. It now also produces an HTML report. - Several functions now use data.table under the hood - Color of the strata containing IS below threshold can now be set in `integration_alluvial_plot()` ## BUG FIXES - Fixed a minor bug in `import_Vispa2_stats()` - function failed when passing `report_path = NULL` - Fixed minor issue in `circos_genomic_density()` when trying to use a pdf device ## DEPRECATED FUNCTIONS - `unzip_file_system()` was made defunct in favor of `generate_default_folder_structure()` - `cumulative_count_union()` was deprecated and its functionality was moved to `cumulative_is()` # ISAnalytics 1.5.3 (2022-01-13) ## MINOR CHANGES - Added arguments `fragmentEstimate_column` and `fragmentEstimate_threshold` in `HSC_population_size_estimate()`. Slightly revised filtering logic. - Updated package logo and website # ISAnalytics 1.5.2 (2021-12-14) ## NEW (MINOR) - Added function to check for annotation problems in IS matrices ## MINOR CHANGES - Added argument `max_workers` in function `remove_collisions()` - Updated default functions for `aggregate_metadata()` - Added annotation issues section in import matrices report ## FIXES - Fixed minor issue in internals for file system alignment checks - Fixed minor issue in internal call to `import_Vispa2_stats()` from `import_association_file()` - Added safe computation of sharing in `remove_collisions()`: if process fails function doesn’t stop # ISAnalytics 1.5.1 (2021-10-28) ## FIXES - Attempt to fix issues with parallel computation on Windows for some plotting functions # ISAnalytics 1.3.9 (2021-10-25) ## FIXES - Fixed issues with function that make use of BiocParallel that sometimes failed on Windows platform # ISAnalytics 1.3.7 (2021-10-20) ## NEW - Added new feature `iss_source()` ## FIXES - Fixed minor issues in data files `refGenes_mm9` and function `compute_near_integrations()` # ISAnalytics 1.3.6 (2021-10-05) ## NEW - Added new feature `purity_filter()` ## FIXES - Fixed small issue in printing information in reports # ISAnalytics 1.3.5 (2021-09-21) ## MAJOR CHANGES - Reworked `is_sharing()` function, detailed usage in vignette `vignette("sharing_analyses", package = "ISAnalytics")` ## NEW - New function `cumulative_is()` - New function for plotting sharing as venn/euler diagrams `sharing_venn()` # ISAnalytics 1.3.4 (2021-08 -03) ## FIXES/MINOR UPDATES - Fixed issue in tests that lead to broken build - Slightly modified included data set for better examples # ISAnalytics 1.3.3 (2021-07-30) ## MAJOR CHANGES - Completely reworked interactive HTML report system, for details take a look at the new vignette `vignette("report_system", package = "ISAnalytics")` - Old `ISAnalytics.widgets` option has been replaced by `ISAnalytics.reports` - In `remove_collisions()`, removed arguments `seq_count_col`, `max_rows_reports` and `save_widget_path`, added arguments `quant_cols` and `report_path` (see documentation for details) ## MINOR CHANGES - `import_single_Vispa2Matrix()` now allows keeping additional non-standard columns - `compute_near_integrations()` is now faster on bigger data sets - Changed default values for arguments `columns` and `key` in `compute_abundance()` - `compute_near_integrations()` now produces only re-calibration map in \*.tsv format - `CIS_grubbs()` now supports calculations for each group specified in argument `by` - In `sample_statistics()` now there is the option to include the calculation of distinct integration sites for each group (if mandatory vars are present) ## NEW FUNCTIONALITY - Added new plotting function `circos_genomic_density()` ## FIXES - Fixed minor issue with NA values in alluvial plots ## DEPRECATIONS - `import_parallel_Vispa2Matrices_interactive()` and `import_parallel_Vispa2Matrices_auto()` are officially deprecated in favor of `import_parallel_Vispa2Matrices()` ## OTHER - The package has now a more complete and functional example data set for executable examples - Reworked documentation # ISAnalytics 1.3.2 (2021-06-28) ## FIXES - Corrected issues in man pages # ISAnalytics 1.3.1 (2021-06-24) ## NEW FUNCTIONALITY - `is_sharing` computes the sharing of IS between groups - `sharing_heatmap` allows visualization of sharing data through heatmaps - `integration_alluvial_plot` allows visualization of integration sites distribution in groups over time. - `top_abund_tableGrob` can be used in combination with the previous function or by itself to obtain a summary of top abundant integrations as an R graphic (tableGrob) object that can be combined with plots. ## MINOR UPDATES - Added more default stats functions to `default_stats` - Added optional automatic conversion of time points in months and years when importing association file - Minor fixes in `generate_Vispa2_launch_AF` # ISAnalytics 1.1.11 (2021-05-11) ## NEW FUNCTIONALITY - `HSC_population_size_estimate` and `HSC_population_plot` allow estimates on hematopoietic stem cell population size - Importing of Vispa2 stats per pool now has a dedicated function, `import_Vispa2_stats` - `outlier_filter` and `outliers_by_pool_fragments` offer a mean to filter poorly represented samples based on custom outliers tests ## VISIBLE USER CHANGES - The argument `import_stats` of `aggregate_metadata` is officially deprecated in favor of `import_Vispa2_stats` - `aggregate_metadata` is now a lot more flexible on what operations can be performed on columns via the new argument `aggregating_functions` - `import_association_file` allows directly for the import of Vispa2 stats and converts time points to months and years where not already present - File system alignment of `import_association_file` now produces 3 separate columns for paths - `separate_quant_matrices` and `comparison_matrix` now do not require mandatory columns other than the quantifications - this allows for separation or joining also for aggregated matrices ## FIXES - Fixed a minor issue in `CIS_volcano_plot` that caused duplication of some labels if highlighted genes were provided in input # ISAnalytics 1.1.10 (2021-04-08) ## FIXES - Fixed issue in `compute_near_integrations`: when provided recalibration map export path as a folder now the function works correctly and produces an automatically generated file name - Fixed issue in `aggregate_metadata`: now paths to folder that contains Vispa2 stats is looked up correctly. Also, VISPA2 stats columns are aggregated if found in the input data frame independently from the parameter `import_stats`. ## IMPROVEMENTS - `compute_abundance` can now take as input aggregated matrices and has additional parameters to offer more flexibility to the user. Major updates and improvements also on documentation and reproducible examples. - Major improvements in function `import_single_Vispa2Matrix`: import is now preferentially carried out using `data.table::fread` greatly speeding up the process - where not possible `readr::read_delim` is used instead - Major improvements in function `import_association_file`: greatly improved parsing precision (each column has a dedicated type), import report now signals parsing problems and their location and signals also problems in parsing dates. Report also includes potential problems in column names and signals missing data in important columns. Added also the possibility to give various file formats in input including `*.xls(x)` formats. - Function `top_integrations` can now take additional parameters to compute top n genes for each specified group - Removed faceting parameters in `CIS_volcano_plot` due to poor precision (easier to add faceting manually) and added parameters to return the data frame that generated the plot as an additional result. Also, it is now possible to specify a vector of gene names to highlight even if they’re not above the annotation threshold. ## MINOR - ISAnalytics website has improved graphic theme and has an additional button on the right that leads to the devel (or release) version of the website - Updated vignettes ## FOR DEVS ONLY - Complete rework of test suite to be compliant to testthat v.3 # ISAnalytics 1.1.9 (2021-02-17) ## FIXES - Fixed minor issues in internal functions with absolute file paths & corrected typos # ISAnalytics 1.1.8 (2020-02-15) ## FIXES - Fixed minor issues in internal functions to optimize file system alignment # ISAnalytics 1.1.7 (2020-02-10) ## FIXES - Fixed minor issues in import_association_file when checking parameters # ISAnalytics 1.1.6 (2020-02-06) ## UPGRADES - It is now possible to save html reports to file from import_parallel_Vispa2Matrices_auto and import_parallel_Vispa2Matrices_interactive, remove_collisions and compute_near_integrations ## FIXES - Fixed sample_statistics: now functions that have data frame output do not produce nested tables. Flat tables are ready to be saved to file or can be nested. - Simplified association file check logic in remove_collisions: now function blocks only if the af doesn’t contain the needed columns # ISAnalytics 1.1.5 (2020-02-03) ## UPGRADES - Upgraded import_association_file function: now file alignment is not mandatory anymore and it is possible to save the html report to file - Updated vignettes and documentation # ISAnalytics 1.1.4 (2020-11-16) ## UPGRADES - Greatly improved reports for collision removal function - General improvements for all widget reports # 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 </details> # Getting help For help please contact the maintainer of the package or open an issue on GitHub.