Bioconductor - MungeSumstats

Bioconductor - MungeSumstats
Bioconductor 3.22
Software Packages
MungeSumstats
MungeSumstats
This is the
released
version of MungeSumstats; for the devel version, see
MungeSumstats
Standardise summary statistics from GWAS
DOI:
10.18129/B9.bioc.MungeSumstats
Bioconductor version:
Release (3.22)
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]
ORCID: 0000-0002-2487-8753
, Brian Schilder [aut, ctb]
ORCID: 0000-0001-5949-2191
, Nathan Skene [aut]
ORCID: 0000-0002-6807-3180
Maintainer:
Alan Murphy
Citation (from within R, enter
citation("MungeSumstats")
):
Installation
To install this package, start R (version "4.5") 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
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
ComparativeGenomics
Genetics
GenomeWideAssociation
GenomicVariation
Preprocessing
SNP
Software
WholeGenome
Version
1.18.1
In Bioconductor since
BioC 3.13 (R-4.1) (5 years)
License
Artistic-2.0
Depends
R (>= 4.1)
Imports
data.table
, utils,
R.utils
dplyr
, stats,
GenomicRanges
GenomeInfoDb
IRanges
ieugwasr
(>= 1.0.1),
BSgenome
Biostrings
stringr
VariantAnnotation
, methods, parallel,
rtracklayer
(>= 1.59.1),
RCurl
System Requirements
URL
Bug Reports
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_1.18.1.tar.gz
Windows Binary (x86_64)
MungeSumstats_1.18.1.zip
(64-bit only)
macOS Binary (x86_64)
MungeSumstats_1.18.1.tgz
macOS Binary (arm64)
MungeSumstats_1.18.1.tgz
Source Repository
git clone https://git.bioconductor.org/packages/MungeSumstats
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/MungeSumstats
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