update RELEASE version number

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bambu
 Type: Package
 Title: Context-Aware Transcript Quantification from Long Read RNA-Seq data
-Version: 3.2.3
+Version: 3.2.4
 Authors@R: c(person("Ying", "Chen", role = c("cre","aut"),
              email = "[email protected]"),
              person("Andre", "Sim", role = "aut",

README.md

@@ -486,31 +486,38 @@ rowData(se)
 ### Release History
 
 **bambu v3.2.6**
+
 Release date: 2023-Apr-26
+
 Minor changes:
-    * Fixes crash during Low Memory Mode when there are scaffolds with no reads
-    * Fixes crash on windows machines caused by DNAStringSet
-    * Adds NDR metadata when running discovery mode with recommended NDR, so users do not need to look at console for the recommended NDR.
-    * Re-enabled GitHub actions for new devel branch name and the windows check
-    * Fixed a crash that occurs with large datasets resulting in large overflow tables during novel gene id assignment
-    * Remove nested bplapply in EM
-    * Remove unused eqClassById list column in the readClassDist object to reduce memory usage
-    * Fixed a bug that caused identical unspliced reads to not be tracked when trackReads = TRUE
+
+- Fixes crash during Low Memory Mode when there are scaffolds with no reads
+- Fixes crash on windows machines caused by DNAStringSet
+- Adds NDR metadata when running discovery mode with recommended NDR, so users do not need to look at console for the recommended NDR.
+- Re-enabled GitHub actions for new devel branch name and the windows check
+- Fixed a crash that occurs with large datasets resulting in large overflow tables during novel gene id assignment
+- Remove nested bplapply in EM
+- Remove unused eqClassById list column in the readClassDist object to reduce memory usage
+- Fixed a bug that caused identical unspliced reads to not be tracked when trackReads = TRUE
 
 **bambu version 3.0.0**
+
 Release date: 2022-10-25
+
 Major changes:
-    * Updated the input parameters of Bambu to simplify the user experience
-    * Introduced NDR threshold recommendation 
-    * Implemented trainBambu(), allowing users to train and use models on their own data
-    * Reads that cannot be assigned to any transcript are grouped as incompatible counts
-    * Partial estimates are removed from output as it can be directly obtained based on total count estimates and full-length count estimates
-    * The fusion mode is now available, which assigns read classes that align to multiple genes to a new combined fusion gene
+
+- Updated the input parameters of Bambu to simplify the user experience
+- Introduced NDR threshold recommendation 
+- Implemented trainBambu(), allowing users to train and use models on their own data
+- Reads that cannot be assigned to any transcript are grouped as incompatible counts
+- Partial estimates are removed from output as it can be directly obtained based on total count estimates and full-length count estimates
+- The fusion mode is now available, which assigns read classes that align to multiple genes to a new combined fusion gene
 
 Minor changes:
-    * Novel transcripts and genes are now by default output with a Bambu prefix
-    * Updated the documentation, messages and errors output by Bambu
-    * Annotated transcripts (with unique exon-junctions) with at least 1 full-length read are assigned a NDR rank
+
+- Novel transcripts and genes are now by default output with a Bambu prefix
+- Updated the documentation, messages and errors output by Bambu
+- Annotated transcripts (with unique exon-junctions) with at least 1 full-length read are assigned a NDR rank
 
 **bambu version 1.99.0**
 
@@ -572,7 +579,7 @@ Release date: 2020-06-18
 Release date: 2020-05-29 
 
 ### Citation
-Chen, Ying, et al. "Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu" bioRxiv (2022). doi: https://doi.org/10.1101/2022.11.14.516358
+Chen, Y., Sim, A., Wan, Y.K. et al. Context-aware transcript quantification from long-read RNA-seq data with Bambu. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01908-w
 
 ### Contributors
 

inst/CITATION

@@ -1,5 +1,5 @@
 citEntry(entry="article",
-         title = "Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu",
+         title = "Context-aware transcript quantification from long-read RNA-seq data with Bambu",
          author = personList( as.person("Ying Chen"),
                               as.person("Andre Sim"),
                               as.person("Yuk Kei Wan"),
@@ -8,10 +8,10 @@ citEntry(entry="article",
                               as.person("Min Hao Ling"),
                               as.person("Michael I. Love"),
                               as.person("Jonathan Göke")),
-         year = 2022,
-         journal = "bioRxiv",
-         doi = "https://doi.org/10.1101/2022.11.14.516358",
+         year = 2023,
+         journal = "Nature Methods",
+         doi = "https://doi.org/10.1038/s41592-023-01908-w",
          textVersion = 
-         paste("Chen, Y., Sim, A. D., Wan, Y. K., Yeo, K., Lee, J. J. X., Ling, M. H., ... & Göke, J.", 
-               "Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu",
-                "bioRxiv (2022)" ) )
+         paste("Chen, Y., Sim, A., Wan, Y. K., Yeo, K., Lee, J. J. X., Ling, M. H., Love, M. I. & Göke, J.", 
+               "Context-aware transcript quantification from long-read RNA-seq data with Bambu",
+                "Nat Methods (2023)" ) )