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[FIX] Fixes for issues with BiocParallel on Windows - bump to 1.5.1

Giulia Pais authored on 28/10/2021 09:46:19
Showing7 changed files

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 Package: ISAnalytics
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 Title: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
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-Version: 1.5.0
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+Version: 1.5.1
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 Date: 2020-07-03
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 Authors@R: c(
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   person(given = "Andrea",
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@@ -2,6 +2,12 @@
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 title: "NEWS"
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 output: github_document
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 ---
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+# ISAnalytics 1.5.1 (2021-10-28)
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+
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+## FIXES
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+
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+* Attempt to fix issues with parallel computation on Windows for some plotting functions
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+
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 # ISAnalytics 1.3.9 (2021-10-25)
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 ## FIXES
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 NEWS
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 ================
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+# ISAnalytics 1.5.1 (2021-10-28)
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+
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+## FIXES
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+
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+-   Attempt to fix issues with parallel computation on Windows for some
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+    plotting functions
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+
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 # ISAnalytics 1.3.9 (2021-10-25)
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 ## FIXES
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@@ -222,7 +229,7 @@ NEWS
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 ## FIXES
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--   Fixed minor issues in import\_association\_file when checking
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+-   Fixed minor issues in import_association_file when checking
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     parameters
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 # ISAnalytics 1.1.6 (2020-02-06)
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@@ -230,25 +237,24 @@ NEWS
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 ## UPGRADES
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 -   It is now possible to save html reports to file from
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-    import\_parallel\_Vispa2Matrices\_auto and
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-    import\_parallel\_Vispa2Matrices\_interactive, remove\_collisions
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-    and compute\_near\_integrations
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+    import_parallel_Vispa2Matrices_auto and
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+    import_parallel_Vispa2Matrices_interactive, remove_collisions and
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+    compute_near_integrations
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 ## FIXES
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--   Fixed sample\_statistics: now functions that have data frame output
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+-   Fixed sample_statistics: now functions that have data frame output
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     do not produce nested tables. Flat tables are ready to be saved to
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     file or can be nested.
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--   Simplified association file check logic in remove\_collisions: now
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+-   Simplified association file check logic in remove_collisions: now
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     function blocks only if the af doesn’t contain the needed columns
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 # ISAnalytics 1.1.5 (2020-02-03)
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 ## UPGRADES
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--   Upgraded import\_association\_file function: now file alignment is
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-    not mandatory anymore and it is possible to save the html report to
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-    file
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+-   Upgraded import_association_file function: now file alignment is not
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+    mandatory anymore and it is possible to save the html report to file
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 -   Updated vignettes and documentation
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 # ISAnalytics 1.1.4 (2020-11-16)
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@@ -288,7 +294,7 @@ NEWS
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     environments that do not have access to a browser)
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 -   Other minor fixes (typos)
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 -   Bug fixes: fixed a few bugs in importing and recalibration functions
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--   Minor fix in import\_association\_file file function: added multiple
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+-   Minor fix in import_association_file file function: added multiple
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     strings to be translated as NA
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 ## IMPORTANT NOTES
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@@ -370,7 +376,7 @@ ISanalytics is officially on bioconductor!
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 -   Added functionality: aggregate functions
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 -   Added vignette on aggregate functions
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 -   Added recalibration functions
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--   Added first analysis function (compute\_abundance)
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+-   Added first analysis function (compute_abundance)
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 ## SIGNIFICANT USER-VISIBLE CHANGES
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@@ -514,19 +514,11 @@ integration_alluvial_plot <- function(x,
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         purrr::set_names(group_names)
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     # Compute plots in parallel
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-    p <- if (.Platform$OS.type == "windows") {
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-        BiocParallel::SnowParam(
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-            stop.on.error = FALSE,
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-            progressbar = TRUE,
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-            tasks = length(groups_to_plot),
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-            exportglobals = TRUE
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-        )
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-    } else {
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-        BiocParallel::MulticoreParam(
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+    p <- BiocParallel::MulticoreParam(
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             stop.on.error = FALSE, progressbar = TRUE,
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             tasks = length(groups_to_plot), exportglobals = FALSE
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         )
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-    }
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+
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     FUN <- function(group_df,
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     plot_x,
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@@ -88,7 +88,7 @@ if (!require(devtools)) {
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   install.packages("devtools")
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 }
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 devtools::install_github("calabrialab/ISAnalytics",
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-                         ref = "RELEASE_3_13",
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+                         ref = "RELEASE_3_14",
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                          dependencies = TRUE,
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                          build_vignettes = TRUE)
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 ```
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@@ -137,6 +137,13 @@ options("ISAnalytics.reports" = TRUE)
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 Show more
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 </summary>
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+# ISAnalytics 1.5.1 (2021-10-28)
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+
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+## FIXES
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+
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+-   Attempt to fix issues with parallel computation on Windows for some
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+    plotting functions
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+
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 # ISAnalytics 1.3.9 (2021-10-25)
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 ## FIXES
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@@ -358,7 +365,7 @@ Show more
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 ## FIXES
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--   Fixed minor issues in import\_association\_file when checking
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+-   Fixed minor issues in import_association_file when checking
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     parameters
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 # ISAnalytics 1.1.6 (2020-02-06)
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@@ -366,25 +373,24 @@ Show more
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 ## UPGRADES
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 -   It is now possible to save html reports to file from
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-    import\_parallel\_Vispa2Matrices\_auto and
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-    import\_parallel\_Vispa2Matrices\_interactive, remove\_collisions
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-    and compute\_near\_integrations
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+    import_parallel_Vispa2Matrices_auto and
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+    import_parallel_Vispa2Matrices_interactive, remove_collisions and
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+    compute_near_integrations
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 ## FIXES
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--   Fixed sample\_statistics: now functions that have data frame output
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+-   Fixed sample_statistics: now functions that have data frame output
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     do not produce nested tables. Flat tables are ready to be saved to
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     file or can be nested.
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--   Simplified association file check logic in remove\_collisions: now
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+-   Simplified association file check logic in remove_collisions: now
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     function blocks only if the af doesn’t contain the needed columns
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 # ISAnalytics 1.1.5 (2020-02-03)
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 ## UPGRADES
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--   Upgraded import\_association\_file function: now file alignment is
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-    not mandatory anymore and it is possible to save the html report to
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-    file
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+-   Upgraded import_association_file function: now file alignment is not
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+    mandatory anymore and it is possible to save the html report to file
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 -   Updated vignettes and documentation
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 # ISAnalytics 1.1.4 (2020-11-16)
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@@ -424,7 +430,7 @@ Show more
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     environments that do not have access to a browser)
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 -   Other minor fixes (typos)
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 -   Bug fixes: fixed a few bugs in importing and recalibration functions
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--   Minor fix in import\_association\_file file function: added multiple
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+-   Minor fix in import_association_file file function: added multiple
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     strings to be translated as NA
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 ## IMPORTANT NOTES
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@@ -506,7 +512,7 @@ ISanalytics is officially on bioconductor!
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 -   Added functionality: aggregate functions
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 -   Added vignette on aggregate functions
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 -   Added recalibration functions
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--   Added first analysis function (compute\_abundance)
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+-   Added first analysis function (compute_abundance)
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 ## SIGNIFICANT USER-VISIBLE CHANGES
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@@ -58,15 +58,11 @@ reference:
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 - contents:
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   - aggregate_metadata
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   - aggregate_values_by_key
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-- title: "Collision removal functions"
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+- title: "Data cleaning and pre-processing"
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 - contents:
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+  - compute_near_integrations
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   - remove_collisions
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   - realign_after_collisions
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-- title: "Recalibration functions"
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-- contents:
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-  - compute_near_integrations
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-- title: "Removal of outliers from raw reads"
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-- contents:
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   - outlier_filter
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   - outliers_by_pool_fragments
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 - title: "Analysis functions"
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@@ -132,4 +128,3 @@ reference:
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   - refGenes_hg19
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   - refGenes_mm9
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   - tumor_suppressors
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-
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@@ -47,7 +47,7 @@ if (!require(devtools)) {
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   install.packages("devtools")
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 }
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 devtools::install_github("calabrialab/ISAnalytics",
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-                         ref = "RELEASE_3_13",
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+                         ref = "RELEASE_3_14",
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                          dependencies = TRUE,
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                          build_vignettes = TRUE)
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 ```