Package: bambu 3.15.0

Introduction | Quick start: Transcript discovery and quantification with bambu | Installation | General Usage | A complete workflow to identify and quantify transcript expression from Nanopore RNA-Seq data | Input data | Aligned reads (bam files) | Genome sequence (fasta file/ BSGenome object) | Genome annotations (bambu annotations object/ gtf file / TxDb object) | Transcript discovery and quantification | Running bambu | Running multiple samples | Modulating the sensitivity of discovery (pre and post analysis) | Visualise results | Obtain gene expression estimates from transcript expression | Save data (gtf/text) | Advanced usages for different use cases | Using a pre-trained model | De-novo transcript discovery | Storing and using preprocessed files (rcFiles) | Tracking read-to-transcript assignment | Training a model on another species/dataset and applying it | Including single exons | Downstream analysis | Identifying differentially expressed genes | Identifying differential transcript usage | Getting help | Citing bambu | Session Information