From f41412e4acbbb70fbbd8695e369b71141875d728 Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Wed, 14 Jun 2023 15:52:39 +0800 Subject: [PATCH 1/4] re-format release history --- README.md | 41 ++++++++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 3cebd8cd..e4e11942 100755 --- a/README.md +++ b/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** From bd262d071cca29b11e01808a5e7d43b0f998c109 Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Wed, 14 Jun 2023 15:54:10 +0800 Subject: [PATCH 2/4] update citation link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e4e11942..92e1ec74 100755 --- a/README.md +++ b/README.md @@ -579,7 +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 From 754a99bf0edf192bb7134f5424a67311ce637608 Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Wed, 14 Jun 2023 16:11:40 +0800 Subject: [PATCH 3/4] update bioconductor citation --- inst/CITATION | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/inst/CITATION b/inst/CITATION index a5b8222f..52dc81de 100644 --- a/inst/CITATION +++ b/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)" ) ) \ No newline at end of file + 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)" ) ) From ffa53178915bc4f939f80f489a511f1b1861a27c Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Wed, 14 Jun 2023 16:32:12 +0800 Subject: [PATCH 4/4] update devel version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0576143f..b9a27a42 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: bambu Type: Package Title: Context-Aware Transcript Quantification from Long Read RNA-Seq data -Version: 3.3.2 +Version: 3.3.3 Authors@R: c(person("Ying", "Chen", role = c("cre","aut"), email = "chen_ying@gis.a-star.edu.sg"), person("Andre", "Sim", role = "aut",