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NEWS
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bambu v3.2.0 (change date: 2023-Apr-26)
==========================================
Minor fixes:
* 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 v3.0.8 (change date: 2023-02-14)
==========================================
Minor fixes:
* Bug fix for writeOutput function to remove unused argument due to dplyr package update
* Correct CPM calculation to incorporate incompatible reads
* Round up quantification estimates to 5 digits (customisable through opt.em argument)
bambu v3.0.0 (Change 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 and used to calculate more accurate gene expression estimates
* The fusion mode is now available, which assigns read classes that align to multiple genes to a new combined fusion gene
* Improved quantification processing time by reorganising quantification steps
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
* Partial estimates are removed from output as it can be directly obtained based on total count estimates and full-length count estimates
bambu v2.2.0 (Change date: 2022-04-27)
===========================================
Major changes:
* Implemented a de-novo mode where no annotation is provided
* Implemented trackReads to allow users to track read to transcript model map
* Implemented outputDistTable to output the distance metrics bedtween read class and transcript models
* Allow input files without specific extension for fasta and annotation gtf files (gff etc)
Minor fixes:
* Fix the bug when reads are aligned outside the supplied genome and
* Provides a warning and issues with bsgenome and their strand.
* Provides a more informative error when running in denovo mode if no transcripts pass the threshold
* Fix bug in runs where annotation gene names had "gene"
bambu v2.0.4 (Change date: 2022-02-08)
===========================================
Minor fixes:
* Fix out of bounds aligned reads bug
* Fix bsgenome strand bug
* Make error clear when in the de novo mode and threshold is too low
* Move NDR out of discovery parameters list
bambu v2.0.3 (Change date: 2022-01-30)
===========================================
Minor fixes:
* Skip the errors when txScore is not calculated
bambu v2.0.1 (Change date: 2022-11-23)
===========================================
Minor fixes:
* Update saved objects using updated Bioc 3.14 packages
bambu v2.0.0 (Change date: 2021-10-18)
=============
Major Changes:
* Implemented a machine learning model to estimate transcript-level novel discovery rate
* Implemented full length estimates, partial length estimates and unique read counts in final output
* Improved the performance for the extend-annotations module with simplified code
* Improved the performance when large amounts of annotations are missing.
* Implemented a lowMemory option to reduce the memory requirements for very large samples (>100 million reads)
Minor fixes:
* Remove the use of get() which looks into environment variables (prone to crashes if a variable of the same name exists) and directly references the functions that should be used instead.
* Fixed the error when a .fa file is provided as a string variable in non-windows system
* Fixed the error when no single exon read class is provided in any samples
* Fixed the bug when no splice overlap is found between read classes and annotations
bambu v1.0.2 (Change date: 2020-11-10)
==============
Changes:
* Bug fix for author name display
* Bug fix for calling fasta file and bam file from ExperimentHub
* Update NEWS file
bambu v1.0.1 (Change date: 2020-11-06)
==============
Changes:
* Bug fix for parallel computation to avoid bplapply
bambu v0.99.4 (Release date: 2020-08-18)
==============
Changes:
* Remove codes using seqlevelStyle to allow customized annotation
* update the requirement of R version and ExperimentHub version
bambu v0.99.1 (Release date: 2020-08-18)
==============
* First submission to BioConductor