- recipe bioconductor-outrider
OUTRIDER - OUTlier in RNA-Seq fInDER
- Homepage:
https://bioconductor.org/packages/3.18/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:
1.20.1-0,1.20.0-0,1.18.1-0,1.16.0-1,1.16.0-0,1.12.0-2,1.12.0-1,1.12.0-0,1.10.0-0,1.20.1-0,1.20.0-0,1.18.1-0,1.16.0-1,1.16.0-0,1.12.0-2,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.0.2-0,1.0.1-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-deseq2:
>=1.42.0,<1.43.0- depends bioconductor-deseq2:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicfeatures:
>=1.54.1,<1.55.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-pcamethods:
>=1.94.0,<1.95.0- depends bioconductor-pcamethods:
>=1.94.0,<1.95.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-bbmisc:
- depends r-data.table:
- depends r-generics:
- depends r-ggplot2:
- depends r-ggrepel:
- depends r-heatmaply:
- depends r-matrixstats:
- depends r-pheatmap:
- depends r-plotly:
- depends r-plyr:
- depends r-prroc:
- depends r-rcolorbrewer:
- depends r-rcpp:
- depends r-rcpparmadillo:
- depends r-reshape2:
- depends r-scales:
- requirements:
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-outrider and update with:: mamba update bioconductor-outrider
To create a new environment, run:
mamba create --name myenvname bioconductor-outrider
with
myenvnamebeing 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-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)
