@@ -1,6 +1,6 @@

 Package: ISAnalytics

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

-Version: 1.5.0

+Version: 1.5.1

 Date: 2020-07-03

 Authors@R: c(

   person(given = "Andrea",

@@ -2,6 +2,12 @@

 title: "NEWS"

 output: github_document

 ---

+# 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

@@ -1,6 +1,13 @@

 NEWS

 ================

+# 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

@@ -222,7 +229,7 @@ NEWS

 ## FIXES

--   Fixed minor issues in import\_association\_file when checking

+-   Fixed minor issues in import_association_file when checking

     parameters

 # ISAnalytics 1.1.6 (2020-02-06)

@@ -230,25 +237,24 @@ NEWS

 ## 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

+    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

+-   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

+-   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

+-   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)

@@ -288,7 +294,7 @@ NEWS

     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

+-   Minor fix in import_association_file file function: added multiple

     strings to be translated as NA

 ## IMPORTANT NOTES

@@ -370,7 +376,7 @@ ISanalytics is officially on bioconductor!

 -   Added functionality: aggregate functions

 -   Added vignette on aggregate functions

 -   Added recalibration functions

--   Added first analysis function (compute\_abundance)

+-   Added first analysis function (compute_abundance)

 ## SIGNIFICANT USER-VISIBLE CHANGES

@@ -514,19 +514,11 @@ integration_alluvial_plot <- function(x,

         purrr::set_names(group_names)

     # Compute plots in parallel

-    p <- if (.Platform$OS.type == "windows") {

-        BiocParallel::SnowParam(

-            stop.on.error = FALSE,

-            progressbar = TRUE,

-            tasks = length(groups_to_plot),

-            exportglobals = TRUE

-        )

-    } else {

-        BiocParallel::MulticoreParam(

+    p <- BiocParallel::MulticoreParam(

             stop.on.error = FALSE, progressbar = TRUE,

             tasks = length(groups_to_plot), exportglobals = FALSE

         )

-    }

+

     FUN <- function(group_df,

     plot_x,

@@ -88,7 +88,7 @@ if (!require(devtools)) {

   install.packages("devtools")

 }

 devtools::install_github("calabrialab/ISAnalytics",

-                         ref = "RELEASE_3_13",

+                         ref = "RELEASE_3_14",

                          dependencies = TRUE,

                          build_vignettes = TRUE)

 ```

@@ -137,6 +137,13 @@ options("ISAnalytics.reports" = TRUE)

 Show more

 </summary>

+# 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

@@ -358,7 +365,7 @@ Show more

 ## FIXES

--   Fixed minor issues in import\_association\_file when checking

+-   Fixed minor issues in import_association_file when checking

     parameters

 # ISAnalytics 1.1.6 (2020-02-06)

@@ -366,25 +373,24 @@ Show more

 ## 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

+    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

+-   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

+-   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

+-   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)

@@ -424,7 +430,7 @@ Show more

     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

+-   Minor fix in import_association_file file function: added multiple

     strings to be translated as NA

 ## IMPORTANT NOTES

@@ -506,7 +512,7 @@ ISanalytics is officially on bioconductor!

 -   Added functionality: aggregate functions

 -   Added vignette on aggregate functions

 -   Added recalibration functions

--   Added first analysis function (compute\_abundance)

+-   Added first analysis function (compute_abundance)

 ## SIGNIFICANT USER-VISIBLE CHANGES

@@ -58,15 +58,11 @@ reference:

 - contents:

   - aggregate_metadata

   - aggregate_values_by_key

-- title: "Collision removal functions"

+- title: "Data cleaning and pre-processing"

 - contents:

+  - compute_near_integrations

   - remove_collisions

   - realign_after_collisions

-- title: "Recalibration functions"

-- contents:

-  - compute_near_integrations

-- title: "Removal of outliers from raw reads"

-- contents:

   - outlier_filter

   - outliers_by_pool_fragments

 - title: "Analysis functions"

@@ -132,4 +128,3 @@ reference:

   - refGenes_hg19

   - refGenes_mm9

   - tumor_suppressors

-

@@ -47,7 +47,7 @@ if (!require(devtools)) {

   install.packages("devtools")

 }

 devtools::install_github("calabrialab/ISAnalytics",

-                         ref = "RELEASE_3_13",

+                         ref = "RELEASE_3_14",

                          dependencies = TRUE,

                          build_vignettes = TRUE)

 ```