---
title: "NEWS"
output: github_document
---
# ISAnalytics 1.4.1 (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* Old `ISAnalytics.widgets` option has been replaced by `ISAnalytics.reports`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
