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