midasHLA

DOI: 10.18129/B9.bioc.midasHLA    

R package for immunogenomics data handling and association analysis

Bioconductor version: Release (3.13)

MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.

Author: Christian Hammer [aut], Maciej Migdał [aut, cre]

Maintainer: Maciej Migdał <mcjmigdal at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("midasHLA")

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("midasHLA")

 

HTML	R Script	MiDAS quick start
HTML	R Script	MiDAS tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBiology, Genetics, Software, StatisticalMethod
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	MIT + file LICENCE
Depends	R (>= 4.1), MultiAssayExperiment(>= 1.8.3)
Imports	assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors(>= 0.20.1), stats, SummarizedExperiment(>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3)
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Suggests	broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	midasHLA_1.0.0.tar.gz
Windows Binary	midasHLA_1.0.0.zip
macOS 10.13 (High Sierra)	midasHLA_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/midasHLA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/midasHLA
Package Short Url	https://bioconductor.org/packages/midasHLA/
Package Downloads Report	Download Stats