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bambu

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Alignment, Coverage, DifferentialExpression, FeatureExtraction, GeneExpression, GenomeAnnotation, GenomeAssembly, ImmunoOncology, LongRead, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, Software, Transcription, Transcriptomics
Version 3.4.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
See More
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_3.4.0.tar.gz
Windows Binary bambu_3.4.0.zip (64-bit only)
macOS Binary (x86_64) bambu_3.4.0.tgz
macOS Binary (arm64) bambu_3.4.0.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