bambu

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see bambu.

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Bioconductor version: 3.21

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 gis.a-star.edu.sg>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("bambu")

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

Documentation

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

browseVignettes("bambu")

bambu HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DifferentialExpression, FeatureExtraction, GeneExpression, GenomeAnnotation, GenomeAssembly, ImmunoOncology, LongRead, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, Software, Transcription, Transcriptomics

Version 3.10.1

In Bioconductor since BioC 3.12 (R-4.0) (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

System Requirements

URL https://github.com/GoekeLab/bambu

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

Linking To Rcpp, RcppArmadillo

Enhances parallel

Depends On Me

Imports Me FLAMES

Suggests Me NanoporeRNASeq

Links To Me

Build Report Build Report

Package Archives

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

Source Package bambu_3.10.1.tar.gz

Windows Binary (x86_64) bambu_3.10.1.zip (64-bit only)

macOS Binary (x86_64) bambu_3.10.1.tgz

macOS Binary (arm64) bambu_3.10.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/bambu

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bambu

Bioc Package Browser https://code.bioconductor.org/browse/bambu/

Package Short Url https://bioconductor.org/packages/bambu/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.21 Source Archive