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https://github.com/bioconductor-source/tximport

https://github.com/bioconductor-source/tximport

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Repository

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  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 256 KB
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Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Code of conduct

README.md

tximport

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Description of methods and analysis described in:

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream statistical analysis packages such as edgeR, DESeq2, limma-voom. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

See examples in the vignette.

Notes:

  • tximport as of version 1.3.9 will import inferential replicates (Gibbs samples or bootstrap samples) from Salmon, Sailfish or kallisto.
  • Though we provide here functionality for performing gene-level differential expression using summarized transcript-level estimates, this is does not mean we suggest that users only perform gene-level analysis. Gene-level differential expression can be complemented with transcript- or exon-level analysis. The argument txOut=TRUE can be used to generate transcript-level matrices.

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

DESCRIPTION cran
  • methods * imports
  • stats * imports
  • utils * imports
  • DESeq2 >= 1.11.6 suggests
  • Matrix * suggests
  • TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
  • arrow * suggests
  • edgeR * suggests
  • eds * suggests
  • jsonlite * suggests
  • knitr * suggests
  • limma * suggests
  • matrixStats * suggests
  • readr >= 0.2.2 suggests
  • rhdf5 * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tximportData * suggests