DOI: 10.18129/B9.bioc.bambu    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see bambu.

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Bioconductor version: 3.14

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

Author: Ying Chen [cre, aut], Andre Sim [aut], Yuk Kei Wan [aut], Jonathan Goeke [aut]

Maintainer: Ying Chen <chen_ying at>

Citation (from within R, enter citation("bambu")):


To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script bambu
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Coverage, DifferentialExpression, FeatureExtraction, GeneExpression, GenomeAnnotation, GenomeAssembly, ImmunoOncology, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, Software, Transcription, Transcriptomics
Version 2.0.6
In Bioconductor since BioC 3.12 (R-4.0) (1.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges
Imports BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
LinkingTo Rcpp, RcppArmadillo
Suggests AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub(>= 1.15.3), DESeq2, NanoporeRNASeq, apeglm, utils, DEXSeq
Enhances parallel
Depends On Me
Imports Me
Suggests Me NanoporeRNASeq
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package bambu_2.0.6.tar.gz
Windows Binary (32- & 64-bit)
macOS 10.13 (High Sierra) bambu_2.0.6.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: