Package: hermes
Title: Preprocessing, analyzing, and reporting of RNA-seq data
Type: Package
Date: 2022-05-05
Version: 1.6.0
Authors@R: c(
    person("Daniel", "Sabanés Bové", email = "daniel.sabanes_bove@roche.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("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")
  )
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 | file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
RdMacros: Rdpack, lifecycle
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/insightsengineering/hermes/
BugReports: https://github.com/insightsengineering/hermes/issues
biocViews: RNASeq, DifferentialExpression, Normalization,
        Preprocessing, QualityControl
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
Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown,
        statmod, testthat (>= 2.0), vdiffr, withr
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_scatterplot.R' 'graphs.R' 'join_cdisc.R'
        'normalization.R' 'package.R' 'pca.R' 'pca_cor_samplevar.R'
        'quality.R' 'top_genes.R' 'utils.R'
git_url: https://git.bioconductor.org/packages/hermes
git_branch: RELEASE_3_18
git_last_commit: 068e897
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 21:33:00 UTC; biocbuild
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@roche.com>
Built: R 4.3.2; ; 2023-12-08 19:47:45 UTC; unix
