Recent Releases of bambu
bambu - bambu v3.2.4-Bioconductor release
Changes since last release v2.0.0
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
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 - 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
- R
Published by cying111 over 2 years ago
bambu - bambu v2.0.0-Bioconductor release
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 when extending annotations 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.
- bug fix when a fa file is provdied as a string variable to non-windows system
- bug fix when no single exon read class in provided samples
- bug fix when no splice overlaps found between read class and annotations
- R
Published by cying111 over 4 years ago
bambu - bambu release version 0.3.0
In this release, we have made the following changes mainly: - fixed the bugs when running on Windows - updated vignettes - updated prepareAnnotations function to allow take in of gtf file - fixed a few other small bugs when running bambu
- R
Published by cying111 over 5 years ago
bambu - bambu release version 0.1.0
Initial Release for bambu
- R
Published by jonathangoeke almost 6 years ago