bambu

DOI: 10.18129/B9.bioc.bambu    

This is the development version of bambu; for the stable release version, see bambu.

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

Bioconductor version: Development (3.13)

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], 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 "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.2
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.0.0), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), IRanges
Imports BiocGenerics, BiocParallel, data.table, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, glmnet, Rsamtools, methods, Rcpp
LinkingTo Rcpp, RcppArmadillo
Suggests AnnotationDbi, Biostrings, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub(>= 1.15.3), DESeq2, NanoporeRNASeq, BSgenome, apeglm, utils, DEXSeq
SystemRequirements
Enhances parallel
URL https://github.com/GoekeLab/bambu
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_1.1.2.tar.gz
Windows Binary bambu_1.1.2.zip
macOS 10.13 (High Sierra) bambu_1.1.2.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

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