midasHLA

DOI: 10.18129/B9.bioc.midasHLA    

This is the development version of midasHLA; for the stable release version, see midasHLA.

R package for immunogenomics data handling and association analysis

Bioconductor version: Development (3.15)

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>

Citation (from within R, enter citation("midasHLA")):

Installation

To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
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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Build Report  

Package Archives

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

Source Package midasHLA_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) midasHLA_1.3.0.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

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