README.md

In bryancquach/omixjutsu: Utilities for omics analysis tasks

R package: omixjutsu

The omixjutsu R package is a suite of utility functions for munging, analyzing, and visualizing various omics data. The following types of tasks are currently supported (more to come!):

• Basic data visualization (histograms, boxplots, barplots, scatterplots, heatmpas, etc.) using a ggplot2 framework.
• Munging and visualization of RNA-seq data processing (read trimming, alignment, transcript quantification, etc.) QC metrics as generated by MultiQC.
• Differential gene expression analysis using DESeq2.
• Differential gene expression analysis using limma and voom.
• Evaluating pairwise variable relationships using correlation metrics, Eta-squared, and Cramer's V.
• Evaluating linear, additive model fit using percentage of explained gene expresion variance (PVE analysis).
• Independent hypothesis weighting for multiple testing correction.

Installation

The most recent development version of this package can be installed using devtools as follows:

devtools::install_github("bryancquach/omixjutsu")

To install a version from a specific commit or branch use the ref option:

# Replace <id> with the desired commit ID (i.e., the SHA hash) or repository branch
devtools::install_github("bryancquach/omixjutsu", ref = "<id>")

# Example for a branch named 'example_branch'
devtools::install_github("bryancquach/omixjutsu", ref = "example_branch")

See this GitHub issue for troubleshooting common sources of installation failures.

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.