Package: bambu 3.9.0

Ying Chen

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

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.

Authors:Ying Chen [cre, aut], Andre Sim [aut], Yuk Kei Wan [aut], Jonathan Goeke [aut]

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bambu.pdf |bambu.html✨
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NEWS

# Install 'bambu' in R:

install.packages('bambu', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/goekelab/bambu/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:bambu-3.7.0(bioc 3.21)bambu-3.8.0(bioc 3.20)

alignment coverage differentialexpression featureextraction geneexpression genomeannotation genomeassembly immunooncology longread multiplecomparison normalization rnaseq regression sequencing software transcription transcriptomics bambu bioconductor long-reads nanopore nanopore-sequencing rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction

8.72 score 189 stars 1 packages 77 scripts 657 downloads 9 exports 86 dependencies

Last updated 22 days agofrom:0a0bfc1b61. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win-x86_64	WARNING	Nov 18 2024
R-4.5-linux-x86_64	WARNING	Nov 18 2024
R-4.4-win-x86_64	WARNING	Nov 18 2024
R-4.4-mac-x86_64	WARNING	Nov 18 2024
R-4.4-mac-aarch64	WARNING	Nov 18 2024
R-4.3-win-x86_64	WARNING	Nov 18 2024
R-4.3-mac-x86_64	WARNING	Nov 18 2024
R-4.3-mac-aarch64	WARNING	Nov 18 2024

Exports:bambu compareTranscripts plotBambu prepareAnnotations readFromGTF trainBambu transcriptToGeneExpression writeBambuOutput writeToGTF

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl data.table DBI DelayedArray dplyr fansi fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png purrr R6 Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr xgboost XML XVector yaml zlibbioc

Analysing Long Read RNA-Seq data with bambu

Ying Chen, Andre Sim, Yuk Kei Wan, Jonathan Göke

Rendered frombambu.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2022-10-28
Started: 2020-04-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
long read isoform reconstruction and quantification	bambu
compare alternatively-spliced transcripts	compareTranscripts
plot.bambu	plotBambu
prepare reference annotations for long read RNA-Seq analysis with Bambu	prepareAnnotations
convert a GTF file into a GRangesList	readFromGTF
Function to train a model for use on other data	trainBambu
transcript to gene expression	transcriptToGeneExpression
Write Bambu results to GTF and transcript/gene-count files	writeBambuOutput
write GRangeslist into GTF file	writeToGTF