Package: bambu
Type: Package
Title: Context-Aware Transcript Quantification from Long Read RNA-Seq
        data
Version: 3.15.1
Authors@R: c(person("Ying", "Chen", role = c("cre","aut"),
             email = "chen_ying@a-star.edu.sg"),
             person("Andre", "Sim", role = "aut",
             email = "andre_sim@a-star.edu.sg"),
             person("Yuk Kei", "Wan", role = "aut",
             email = "Wan_Yuk_Kei@a-star.edu.sg"),
             person("Jonathan", "Goeke", role = "aut",
             email = "Jonathan_GOEKE@a-star.edu.sg"))
Description: 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.
License: GPL-3 + file LICENSE
Encoding: UTF-8
ByteCompile: true
Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
        0.22.1), BSgenome, IRanges
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, purrr, apeglm, utils, DEXSeq
Enhances: parallel
SystemRequirements:
biocViews: Alignment, Coverage, DifferentialExpression,
        FeatureExtraction, GeneExpression, GenomeAnnotation,
        GenomeAssembly, ImmunoOncology, LongRead, MultipleComparison,
        Normalization, RNASeq, Regression, Sequencing, Software,
        Transcription, Transcriptomics
bugReports: https://github.com/GoekeLab/bambu/issues
URL: https://github.com/GoekeLab/bambu
RoxygenNote: 7.2.1
LinkingTo: Rcpp, RcppArmadillo
Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr,
        GenomeInfoDb, GenomicAlignments, GenomicFeatures,
        GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-02 03:47:38 UTC
RemoteUrl: https://github.com/bioc/bambu
RemoteRef: HEAD
RemoteSha: 0b4151559ab50fadc74623e3a5f3a58d210d705f
NeedsCompilation: yes
Packaged: 2026-11-01 08:20:11 UTC; root
Author: Ying Chen [cre, aut],
  Andre Sim [aut],
  Yuk Kei Wan [aut],
  Jonathan Goeke [aut]
Maintainer: Ying Chen <chen_ying@a-star.edu.sg>