bambu

DOI: 10.18129/B9.bioc.bambu    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	bambu
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Coverage, DifferentialExpression, FeatureExtraction, GeneExpression, GenomeAnnotation, GenomeAssembly, ImmunoOncology, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, Software, Transcription, Transcriptomics
Version	2.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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
SystemRequirements
Enhances	parallel
URL	https://github.com/GoekeLab/bambu
Depends On Me
Imports Me	FLAMES
Suggests Me	NanoporeRNASeq
Links To Me
Build Report

Package Archives

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

Source Package	bambu_2.2.0.tar.gz
Windows Binary	bambu_2.2.0.zip (64-bit only)
macOS Binary (x86_64)	bambu_2.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bambu
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bambu
Package Short Url	https://bioconductor.org/packages/bambu/
Package Downloads Report	Download Stats