hermes

DOI: 10.18129/B9.bioc.hermes    

This is the development version of hermes; to use it, please install the devel version of Bioconductor.

Preprocessing, analyzing, and reporting of RNA-seq data

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script Introduction to `hermes`
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, Normalization, Preprocessing, QualityControl, RNASeq, Software
Version 0.99.4
In Bioconductor since BioC 3.15 (R-4.2)
License Apache License 2.0 | file LICENSE
Depends ggfortify, R (>= 4.1), SummarizedExperiment(>= 1.16)
Imports assertthat, biomaRt, Biobase, BiocGenerics, circlize, checkmate, 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
LinkingTo
Suggests BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr
SystemRequirements
Enhances
URL https://github.com/insightsengineering/hermes/
BugReports https://github.com/insightsengineering/hermes/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package hermes_0.99.4.tar.gz
Windows Binary
macOS 10.13 (High Sierra) hermes_0.99.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/hermes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hermes
Package Short Url https://bioconductor.org/packages/hermes/
Package Downloads Report Download Stats

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