Merge pull request #136 from charles-plessy/prepare_2.16.0

Prepare the 2.16.0 release.

Author: charles-plessy

DESCRIPTION

@@ -1,11 +1,12 @@
 Package: CAGEr
 Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
-Version: 2.15.1
-Date: 2025-06-22
+Version: 2.15.2
+Date: 2025-10-10
 Authors@R:
   c( person("Vanja",   "Haberle",   email = "vanja.haberle@gmail.com",       role = "aut"),
      person("Charles", "Plessy",    email = "charles.plessy@oist.jp",        role = "cre"),
      person("Damir",   "Baranasic", email = "damir.baranasic@lms.mrc.ac.uk", role = "ctb"),
+     person("Katalin", "Ferenc",    email = "k.t.ferenc@ncmbm.uio.no",       role = "ctb"),
      person("Sarvesh", "Nikumbh",   email = "s.nikumbh@lms.mrc.ac.uk",       role = "ctb")
   )
 Imports:
@@ -20,7 +21,7 @@ Imports:
     GenomicAlignments (>= 1.45.1),
     GenomicFeatures (>= 1.61.4),
     GenomicRanges (>= 1.61.1),
-    ggplot2 (>= 2.2.0),
+    ggplot2 (>= 4.0.0),
     gtools,
     IRanges (>= 2.18.0),
     KernSmooth,

NEWS.md

@@ -1,3 +1,21 @@
+# Changes in version 2.16.0 (29/10/2025)
+
+NEW FEATURES
+
+- Pass normalised expression values to `quickEnhancers()`. Closes #132.
+- New `correlationMatrix()` function to compute correlation matrix without
+  plotting it.  Closes #129.
+- Save power law alpha value in the `reference.slope` element of the `meta`
+  slot of the _ggplot2_ object produced by `plotReverseCumulatives()`.
+- Support for importing CTSS data from bigWig files.
+
+BUG FIXES
+
+- Stop passing _StitchedGPos_ to `quickEnhancesr()`. Closes #133.
+- Migrate from _GenomeInfoDb_ to _Seqinfo_ where needed.
+
+# No changes in version 2.14.0 (16/04/2025)
+
 # Changes in version 2.12.0 (30/10/2024)
 
 BACKWARDS-INCOMPATIBLE CHANGES

R/ExportMethods.R

@@ -40,7 +40,8 @@ NULL
 #' @returns A [`ggplot2::ggplot`] object containing the plots.  The plot can
 #' be further modified to change its title or axis labels (see
 #' [`ggplot2::labs`]).  The legend can be removed with
-#' [`ggplot2::guides`]`(col=FALSE)`.
+#' [`ggplot2::guides`]`(col=FALSE)`.  The alpha parameter of the power law is
+#' saved in the `reference.slope` element of the `meta` slot of the object.
 #' 
 #' @references Balwierz _et al_. (2009) Methods for analyzing deep sequencing
 #' expression data: constructing the human and mouse promoterome with deepCAGE data,