Package: bambu
Type: Package
Title: Reference-guided isoform reconstruction and quantification for
        long read RNA-Seq data
Version: 1.2.1
Authors@R: c(person("Ying", "Chen", role = c("cre","aut"),
             email = "chen_ying@gis.a-star.edu.sg"),
             person("Yuk Kei", "Wan", role = "aut",
             email = "Wan_Yuk_Kei@gis.a-star.edu.sg"),
             person("Jonathan", "Goeke", role = "aut",
             email = "gokej@gis.a-star.edu.sg"))
Description: 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. 
License: GPL-3 + file LICENSE
Encoding: UTF-8
Depends: R(>= 4.0.0), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
        0.22.1), IRanges
Suggests: AnnotationDbi, Biostrings, BiocFileCache, ggplot2,
        ComplexHeatmap, circlize, ggbio, gridExtra, knitr, rmarkdown,
        testthat, BSgenome.Hsapiens.NCBI.GRCh38,
        TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3),
        DESeq2, NanoporeRNASeq, BSgenome, apeglm, utils, DEXSeq
Enhances: parallel
SystemRequirements:
biocViews: Alignment, Coverage, DifferentialExpression,
        FeatureExtraction, GeneExpression, GenomeAnnotation,
        GenomeAssembly, ImmunoOncology, MultipleComparison,
        Normalization, RNASeq, Regression, Sequencing, Software,
        Transcription, Transcriptomics
bugReports: https://github.com/GoekeLab/bambu/issues
URL: https://github.com/GoekeLab/bambu
RoxygenNote: 7.1.1
LinkingTo: Rcpp, RcppArmadillo
Imports: BiocGenerics, BiocParallel, data.table, dplyr, GenomeInfoDb,
        GenomicAlignments, GenomicFeatures, GenomicRanges, stats,
        glmnet, Rsamtools, methods, Rcpp
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/bambu
git_branch: RELEASE_3_13
git_last_commit: 1c71eae
git_last_commit_date: 2021-08-30
Date/Publication: 2021-08-31
NeedsCompilation: yes
Packaged: 2021-08-31 15:29:41 UTC; biocbuild
Author: Ying Chen [cre, aut],
  Yuk Kei Wan [aut],
  Jonathan Goeke [aut]
Maintainer: Ying Chen <chen_ying@gis.a-star.edu.sg>
Built: R 4.1.1; i386-w64-mingw32; 2021-09-01 11:30:11 UTC; windows
Archs: i386, x64
