hermes
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see hermes.
Preprocessing, analyzing, and reporting of RNA-seq data
Bioconductor version: 3.16
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("hermes")):
Installation
To install this package, start R (version "4.2") 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")| Introduction to `hermes` | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, Normalization, Preprocessing, QualityControl, RNASeq, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 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 |
| System Requirements | |
| URL | https://github.com/insightsengineering/hermes/ |
| Bug Reports | https://github.com/insightsengineering/hermes/issues |
See More
| Suggests | BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | hermes_1.2.0.tar.gz |
| Windows Binary | hermes_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | hermes_1.2.0.tgz |
| macOS Binary (arm64) | hermes_1.2.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |