recipe bioconductor-fraser

Find RAre Splicing Events in RNA-Seq Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/FRASER.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-fraser/meta.yaml

Links:

https: :https:`//doi.org/10.1038/s41467-020-20573-7`

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

package bioconductor-fraser

Versions:

1.10.0-0,  1.6.1-2,  1.6.1-1,  1.6.1-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.1-1,  1.2.1-0, 

1.10.0-0,  1.6.1-2,  1.6.1-1,  1.6.1-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.1-1,  1.2.1-0,  1.2.0-0,  1.0.1-0,  1.0.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-delayedarray >=0.24.0,<0.25.0

• bioconductor-delayedmatrixstats >=1.20.0,<1.21.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-hdf5array >=1.26.0,<1.27.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-outrider >=1.16.0,<1.17.0

• bioconductor-pcamethods >=1.90.0,<1.91.0

• bioconductor-rhdf5 >=2.42.0,<2.43.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rsubread >=2.12.0,<2.13.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-bbmisc

• r-cowplot

• r-data.table

• r-extradistr

• r-generics

• r-ggplot2

• r-ggrepel

• r-matrixstats

• r-pheatmap

• r-plotly

• r-prroc

• r-r.utils

• r-rcolorbrewer

• r-rcpp

• r-rcpparmadillo

• r-tibble

• r-vgam

Required By:

• drop

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-fraser

and update with:

conda update bioconductor-fraser

or use the docker container:

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

(see bioconductor-fraser/tags for valid values for <tag>)

Download stats

Link to this page

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