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hermes

Preprocessing, analyzing, and reporting of RNA-seq data


Bioconductor version: Release (3.18)

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.

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], Simona Rossomanno [aut], Tim Treis [aut], Mark Yan [aut], Naomi Chang [aut], Chendi Liao [aut], Carolyn Zhang [aut], Joseph N. Paulson [aut]

Maintainer: Daniel Sabanés Bové <daniel.sabanes_bove at roche.com>

Citation (from within R, enter citation("hermes")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("hermes")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("hermes")
Introduction to `hermes` HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, Normalization, Preprocessing, QualityControl, RNASeq, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Apache License 2.0 | file LICENSE
Depends ggfortify, R (>= 4.1), SummarizedExperiment(>= 1.16)
Imports assertthat, biomaRt, Biobase, BiocGenerics, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats, GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, stats, S4Vectors, tidyr, utils
System Requirements
URL https://github.com/insightsengineering/hermes/
Bug Reports https://github.com/insightsengineering/hermes/issues
See More
Suggests BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package hermes_1.6.0.tar.gz
Windows Binary hermes_1.6.0.zip
macOS Binary (x86_64) hermes_1.6.0.tgz
macOS Binary (arm64) hermes_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hermes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hermes
Bioc Package Browser https://code.bioconductor.org/browse/hermes/
Package Short Url https://bioconductor.org/packages/hermes/
Package Downloads Report Download Stats