MungeSumstats
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MungeSumstats.
Standardise summary statistics from GWAS
Bioconductor version: 3.17
The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.
Author: Alan Murphy [aut, cre] 
, Brian Schilder [aut, ctb] , Nathan Skene [aut]
Maintainer: Alan Murphy <alanmurph94 at hotmail.com>
citation("MungeSumstats")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MungeSumstats")
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("MungeSumstats")| docker | HTML | R Script |
| MungeSumstats | HTML | R Script |
| OpenGWAS | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1) |
| Imports | magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer(>= 1.59.1), RCurl |
| System Requirements | |
| URL | https://github.com/neurogenomics/MungeSumstats |
| Bug Reports | https://github.com/neurogenomics/MungeSumstats/issues |
See More
| Suggests | SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MungeSumstats_1.8.0.tar.gz |
| Windows Binary | MungeSumstats_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | MungeSumstats_1.8.0.tgz |
| macOS Binary (arm64) | MungeSumstats_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MungeSumstats |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MungeSumstats |
| Bioc Package Browser | https://code.bioconductor.org/browse/MungeSumstats/ |
| Package Short Url | https://bioconductor.org/packages/MungeSumstats/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |