hermes

DOI: 10.18129/B9.bioc.hermes  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see hermes.

Preprocessing, analyzing, and reporting of RNA-seq data

Bioconductor version: 3.17

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>

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")

 

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

Details

biocViews	DifferentialExpression, Normalization, Preprocessing, QualityControl, RNASeq, Software
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 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
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_1.4.0.tar.gz
Windows Binary	hermes_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	hermes_1.4.0.tgz
macOS Binary (arm64)	hermes_1.4.0.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