recipe bioconductor-hermes

Preprocessing, analyzing, and reporting of RNA-seq data

Homepage:

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

License:

Apache License 2.0 | file LICENSE

Recipe:

/bioconductor-hermes/meta.yaml

Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed RNA-seq data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from BioMart. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including `cpm`, `rpkm` and `tpm` can be used, and `DESeq2` as well as `voom` differential expression analyses are available.

package bioconductor-hermes

Versions:

1.2.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-multiassayexperiment >=1.24.0,<1.25.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-assertthat

• r-base >=4.2,<4.3.0a0

• r-checkmate >=2.1

• r-circlize

• r-dplyr

• r-envstats

• r-forcats

• r-ggfortify

• r-ggplot2

• r-ggrepel >=0.9

• r-lifecycle

• r-magrittr

• r-matrixstats

• r-purrr

• r-r6

• r-rdpack

• r-rlang

• r-tidyr

Required By:

Installation

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

conda install bioconductor-hermes

and update with:

conda update bioconductor-hermes

or use the docker container:

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

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

Download stats

Link to this page

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