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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "saseR" in publications use:'
type: software
license: Artistic-2.0
title: 'saseR: Scalable Aberrant Splicing and Expression Retrieval'
version: 1.1.0
abstract: 'saseR is a highly performant and fast framework for aberrant expression
  and splicing analyses. The main functions are: \itemize \item \code\linkBamtoAspliCounts
  - Process BAM files to ASpli counts \item \code\linkconvertASpli - Get gene, bin
  or junction counts from ASpli SummarizedExperiment \item \code\linkcalculateOffsets
  - Create an offsets assays for aberrant expression or splicing analysis \item \code\linksaseRfindEncodingDim
  - Estimate the optimal number of latent factors to include when estimating the mean
  expression \item \code\linksaseRfit - Parameter estimation of the negative binomial
  distribution and compute p-values for aberrant expression and splicing For information
  upon how to use these functions, check out our vignette at \urlhttps://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd
  and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq
  tools for fast scalable differential usage, aberrant splicing and expression analyses.
  bioRxiv. \urlhttps://doi.org/10.1101/2023.06.29.547014.'
authors:
- family-names: Segers
  given-names: Alexandre
  email: Alexandre.segers@ugent.be
repository: https://bioc.r-universe.dev
repository-code: https://github.com/statOmics/saseR
url: https://doi.org/10.1101/2023.06.29.547014
date-released: '2023-06-01'
contact:
- family-names: Segers
  given-names: Alexandre
  email: Alexandre.segers@ugent.be