DESCRIPTION

Type: Package
Package: hermes
Title: Preprocessing, analyzing, and reporting of RNA-seq data
Version: 1.7.2.9004
Date: 2024-12-12
Authors@R: c(
    person("Daniel", "Sabanés Bové", , "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", , "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", , "chendi.liao@roche.com", role = "aut"),
    person("Carolyn Zhang", role = "aut"),
    person("Joseph N.", "Paulson", , "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,
    lifecycle,
    limma,
    magrittr,
    matrixStats,
    methods,
    MultiAssayExperiment,
    purrr,
    R6,
    Rdpack,
    rlang,
    S4Vectors,
    stats,
    tidyr,
    utils
Suggests:
    BiocStyle,
    DelayedArray,
    DT,
    grid,
    httr,
    knitr,
    rmarkdown,
    statmod,
    testthat (>= 2.0),
    vdiffr
VignetteBuilder:
    knitr
RdMacros:
    lifecycle,
    Rdpack
biocViews: RNASeq, DifferentialExpression, Normalization, Preprocessing,
    QualityControl
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
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'