Changes in version 1.4.3 (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 Changes in version 1.4.2 (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 Changes in version 1.4.1 (2021-10-28) FIXES - Attempt to fix issues with parallel computation on Windows for some plotting functions Changes in version 1.3.9 (2021-10-25) FIXES - Fixed issues with function that make use of BiocParallel that sometimes failed on Windows platform Changes in version 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() Changes in version 1.3.6 (2021-10-05) NEW - Added new feature purity_filter() FIXES - Fixed small issue in printing information in reports Changes in version 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() Changes in version 1.3.4 FIXES/MINOR UPDATES - Fixed issue in tests that lead to broken build - Slightly modified included data set for better examples Changes in version 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take a look at the new vignette vignette("report_system", package = "ISAnalytics") - Old ISAnalytics.widgets option has been replaced by ISAnalytics.reports - In remove_collisions(), removed arguments seq_count_col, max_rows_reports and save_widget_path, added arguments quant_cols and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 Changes in version 1.3.2 (2021-06-28) FIXES - Corrected issues in man pages Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.1.9 (2021-02-17) FIXES - Fixed minor issues in internal functions with absolute file paths & corrected typos Changes in version 1.1.8 (2020-02-15) FIXES - Fixed minor issues in internal functions to optimize file system alignment Changes in version 1.1.7 (2020-02-10) FIXES - Fixed minor issues in import_association_file when checking parameters Changes in version 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 Changes in version 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 Changes in version 1.1.4 (2020-11-16) UPGRADES - Greatly improved reports for collision removal function - General improvements for all widget reports Changes in version 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” Changes in version 1.1.2 (2020-11-05) FIXES - Fixed missing restarts for non-blocking widgets Changes in version 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! Changes in version 0.99.14 (2020-10-21) - Minor fixes in tests Changes in version 0.99.13 (2020-10-19) NEW FEATURES - Added analysis functions CIS_grubbs and cumulative_count_union - Added plotting functions CIS_volcano_plot Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 0.99.8 (2020-08-12) - Submitted to Bioconductor