recipe bioconductor-outrider

OUTRIDER - OUTlier in RNA-Seq fInDER

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-outrider/meta.yaml

Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.

package bioconductor-outrider

Versions:

1.16.0-0,  1.12.0-2,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.16.0-0,  1.12.0-2,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.2-0,  1.0.1-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-pcamethods >=1.90.0,<1.91.0

• 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-data.table

• r-generics

• r-ggplot2

• r-heatmaply

• r-matrixstats

• r-pheatmap

• r-plotly

• r-plyr

• r-prroc

• r-rcolorbrewer

• r-rcpp

• r-rcpparmadillo

• r-reshape2

• r-scales

Required By:

• bioconductor-fraser

• drop

Installation

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

conda install bioconductor-outrider

and update with:

conda update bioconductor-outrider

or use the docker container:

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

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

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