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Huntsmanlab / utanos

Utilities for doing analysis on shallow WGS data
https://huntsmanlab.github.io/utanos/
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utanos

Lifecycle: experimental

Package Goal:

To be a swiss army knife in analyzing shallow/low-pass WGS data.

Package Description/Details:

Utilities for The ANalysis Of Shallow WGS in R (UTANOS or utanos). Includes functions for plotting, quality evaluation, data re-structuring, copy-number aberration exploration, copy-number signature inference, and HRD identification. Additionally, there are tools that export analyses/datasets in formats useful for human examination. (i.e. for non-computational purposes).

Installation:

Install R (version > 4.2)
Cran would be the place to find the right R

Ensure the following basic packages are installed.

install.packages("librarian")
BiocManager::install("Biobase")

Install the bulk of this package’s dependencies making use of librarian:

librarian::shelf(caret, CGHcall, data.table, DBI, DescTools, devtools, doMC, dplyr, EnsDb.Hsapiens.v75, flexmix, GenomicRanges, ggalt, ggplot2, ggpubr, ggrepel, gridExtra, hrbrthemes, ks, magrittr, NMF, pheatmap, plyr, purrr, QDNAseq, readr, RMySQL, stringr, tidyr, viridis, YAPSA)

Install annotables from github:

devtools::install_github("stephenturner/annotables")

Finally, install utanos:

install_github("Huntsmanlab/utanos")