- 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:
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
- Required By:
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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-outrider/README.html)