hermes
Preprocessing, analyzing, and reporting of RNA-seq data
Bioconductor version: 3.23 · Package version: 1.16.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("hermes")Details
| Maintainer | Daniel Sabanés Bové <daniel.sabanes_bove@rconis.com> |
| Author | Daniel Sabanés Bové [aut, cre], Namrata Bhatia [aut], Stefanie Bienert [aut], Benoit Falquet [aut], Haocheng Li [aut], Jeff Luong [aut], Lyndsee Midori Zhang [aut], Alex Richardson [aut], Simona Rossomanno [aut], Tim Treis [aut], Mark Yan [aut], Naomi Chang [aut], Chendi Liao [aut], Carolyn Zhang [aut], Joseph N. Paulson [aut], F. Hoffmann-La Roche AG [cph, fnd] |
| License | Apache License 2.0 |
| URL | https://insightsengineering.github.io/hermes/ |
| Bug Reports | https://github.com/insightsengineering/hermes/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, Normalization, Preprocessing, QualityControl, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/hermes/ |
Citation
From within R, enter citation("hermes"):
Daniel Sabanés Bové, Namrata Bhatia, Stefanie Bienert, Benoit Falquet, Haocheng Li, Jeff Luong, Lyndsee Midori Zhang, Alex Richardson, Simona Rossomanno, Tim Treis, Mark Yan, Naomi Chang, Chendi Liao, Carolyn Zhang, Joseph N. Paulson. hermes: Preprocessing, analyzing, and reporting of RNA-seq data. doi:10.18129/B9.bioc.hermes, R package version 1.16.0, https://bioconductor.org/packages/hermes.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | hermes_1.16.0.tar.gz |
| Windows binary (x86_64) | hermes_1.16.0.zip |
| macOS binary (arm64) | hermes_1.16.0.tgz |
| macOS binary (x86_64) | hermes_1.16.0.tgz |
Dependencies
Depends: ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16)
Imports: assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats (>= 1.0.0), GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, limma, magrittr, matrixStats (>= 1.5.0), methods, MultiAssayExperiment, purrr, R6, Rdpack (>= 2.6.2), rlang, S4Vectors, stats, tidyr, utils
Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 3.2.2), vdiffr (>= 1.0.8)