Name Mode Size
..
GeneSpec-class.R 100644 7 kb
HermesData-class.R 100644 6 kb
HermesData-methods.R 100644 26 kb
HermesData-validate.R 100644 3 kb
argument_convention.R 100644 1 kb
assertthat.R 100644 4 kb
calc_cor.R 100644 4 kb
checkmate.R 100644 2 kb
connections.R 100644 12 kb
data.R 100644 3 kb
differential.R 100644 10 kb
dplyr_compatibility.R 100644 1 kb
draw_barplot.R 100644 3 kb
draw_boxplot.R 100644 5 kb
draw_scatterplot.R 100644 3 kb
graphs.R 100644 8 kb
join_cdisc.R 100644 4 kb
normalization.R 100644 9 kb
package.R 100644 1 kb
pca.R 100644 3 kb
pca_cor_samplevar.R 100644 7 kb
quality.R 100644 9 kb
top_genes.R 100644 4 kb
utils.R 100644 11 kb
README.Rmd
--- output: github_document --- <!-- README.md is generated from README.Rmd. Please edit that file --> ```{r, echo = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" ) ``` [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) \ # hermes <p align="center"> <img src='man/figures/logo.png' align="right" height="131.5" alt="hermes-logo"/> </p> > `hermes` facilitates preprocessing, analyzing, and reporting of RNA-seq data. * Imports RNAseq count data into the `hermes` ready format. * Annotates gene information automatically from a central database (e.g. BioMart). * Adds quality control (QC) flags to genes and samples. * Filters the data set. * Normalizes the counts. * Quickly produces descriptive plots. * Performs principal components analysis. * Produces a templated QC report. * Performs differential expression analysis. ## Installation ### BioConductor You can install the current release from BioConductor with: ```{r bioc-installation, eval = FALSE} # install.packages("BiocManager") BiocManager::install("hermes") ``` ### GitHub You can install the development version from GitHub with: ```{r gh-installation, eval = FALSE} # install.packages("devtools") devtools::install_github("insightsengineering/hermes") ``` ## Getting Started You can get started by reading the introduction vignette: ```{r vignette-start, eval = FALSE} library(hermes) vignette("introduction", package = "hermes") ```