Package: hermes
Title: Preprocessing, analyzing, and reporting of RNA-seq data
Type: Package
Date: 2025-09-09
Version: 1.17.0
Authors@R: c(
    person("Daniel", "Sabanés Bové", email = "daniel.sabanes_bove@rconis.com", role = c("aut", "cre")),
    person("Namrata", "Bhatia", role = "aut"),
    person("Stefanie", "Bienert", role = "aut"),
    person("Benoit", "Falquet", role = "aut"),
    person("Haocheng", "Li", role = "aut"),
    person("Jeff", "Luong", role = "aut"),
    person("Lyndsee", "Midori Zhang", email = "zhang.lyndsee@gene.com", role = "aut"),
    person("Alex", "Richardson", role = "aut"),
    person("Simona", "Rossomanno", role = "aut"),
    person("Tim", "Treis", role = "aut"),
    person("Mark", "Yan", role = "aut"),
    person("Naomi", "Chang", role = "aut"),
    person("Chendi", "Liao", email = "chendi.liao@roche.com", role = "aut"),
    person("Carolyn Zhang", role = "aut"),
    person("Joseph N.", "Paulson", email = "paulson.joseph@gene.com", role = "aut"),
    person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
  )
Description: 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.
License: Apache License 2.0
URL: https://insightsengineering.github.io/hermes/
BugReports: https://github.com/insightsengineering/hermes/issues
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)
VignetteBuilder: knitr
RdMacros: Rdpack
biocViews: RNASeq, DifferentialExpression, Normalization,
        Preprocessing, QualityControl
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
Collate: 'GeneSpec-class.R' 'HermesData-validate.R'
        'HermesData-class.R' 'HermesData-methods.R'
        'argument_convention.R' 'assertthat.R' 'calc_cor.R'
        'checkmate.R' 'connections.R' 'data.R' 'differential.R'
        'dplyr_compatibility.R' 'draw_barplot.R' 'draw_boxplot.R'
        'draw_heatmap.R' 'draw_scatterplot.R' 'graphs.R' 'join_cdisc.R'
        'normalization.R' 'package.R' 'pca.R' 'pca_cor_samplevar.R'
        'quality.R' 'top_genes.R' 'utils.R'
Config/pak/sysreqs: libicu-dev libpng-dev libxml2-dev libssl-dev perl
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:57:33 UTC
RemoteUrl: https://github.com/bioc/hermes
RemoteRef: HEAD
RemoteSha: f49637da43a95a7c41468a51cfb575db834228ed
NeedsCompilation: no
Packaged: 2026-07-04 00:08:53 UTC; root
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]
Maintainer: Daniel Sabanés Bové <daniel.sabanes_bove@rconis.com>