bambu
Context-Aware Transcript Quantification from Long Read RNA-Seq data
Bioconductor version: Release (3.19)
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("bambu")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Coverage, DifferentialExpression, FeatureExtraction, GeneExpression, GenomeAnnotation, GenomeAssembly, ImmunoOncology, LongRead, MultipleComparison, Normalization, RNASeq, Regression, Sequencing, Software, Transcription, Transcriptomics |
| Version | 3.6.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_3.6.0.tar.gz |
| Windows Binary (x86_64) | bambu_3.6.0.zip (64-bit only) |
| macOS Binary (x86_64) | bambu_3.6.0.tgz |
| macOS Binary (arm64) | bambu_3.6.0.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 |