recipe bioconductor-saser

Scalable Aberrant Splicing and Expression Retrieval

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/saseR.html

License:

Artistic-2.0

Recipe:

/bioconductor-saser/meta.yaml

saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - 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 \url{https://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. \url{https://doi.org/10.1101/2023.06.29.547014}.

package bioconductor-saser

versions:

1.2.0-0

depends bioconductor-aspli:

>=2.16.0,<2.17.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-dexseq:

>=1.52.0,<1.53.0

depends bioconductor-edger:

>=4.4.0,<4.5.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-dplyr:

depends r-igraph:

depends r-knitr:

depends r-mass:

depends r-pracma:

depends r-precrec:

depends r-prroc:

depends r-rrcov:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-saser

and update with::

   mamba update bioconductor-saser

To create a new environment, run:

mamba create --name myenvname bioconductor-saser

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-saser:<tag>

(see `bioconductor-saser/tags`_ for valid values for ``<tag>``)

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