Bioconductor version: Release (3.15)
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 (from within R,
enter citation("MungeSumstats")
):
To install this package, start R (version "4.2") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MungeSumstats")
HTML | R Script | docker |
HTML | R Script | MungeSumstats |
HTML | R Script | OpenGWAS |
Reference Manual | ||
Text | NEWS |
biocViews | ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome |
Version | 1.4.5 |
In Bioconductor since | BioC 3.13 (R-4.1) (1.5 years) |
License | Artistic-2.0 |
Depends | R (>= 4.1) |
Imports | magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer, RCurl |
LinkingTo | |
Suggests | SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, seqminer, Rsamtools, MatrixGenerics, badger |
SystemRequirements | |
Enhances | |
URL | https://github.com/neurogenomics/MungeSumstats |
BugReports | https://github.com/neurogenomics/MungeSumstats/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | MungeSumstats_1.4.5.tar.gz |
Windows Binary | MungeSumstats_1.4.5.zip (64-bit only) |
macOS Binary (x86_64) | MungeSumstats_1.4.5.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/MungeSumstats |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MungeSumstats |
Package Short Url | https://bioconductor.org/packages/MungeSumstats/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.15 | Source Archive |
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