Package: hmagmaR 0.99.3

Aydan Asgarova

hmagmaR: Incorporation of chromatin interaction and epigenetic profiles to predict risk genes

Combines chromatin interaction (e.g. PLAC-seq/Hi-C) data with regulatory region annotations (e.g. promoters, enhancers, H3K27ac) to link non-coding GWAS SNPs to their putative target genes, producing MAGMA-compatible gene annotation files for downstream gene-level association testing.

Authors:Aydan Asgarova [aut, cre]

hmagmaR_0.99.3.tar.gz
hmagmaR_0.99.3.zip(r-4.7-any)hmagmaR_0.99.3.zip(r-4.6-any)hmagmaR_0.99.3.zip(r-4.5-any)
hmagmaR_0.99.3.tgz(r-4.6-any)hmagmaR_0.99.3.tgz(r-4.5-any)
hmagmaR_0.99.3.tar.gz(r-4.7-any)hmagmaR_0.99.3.tar.gz(r-4.6-any)
hmagmaR_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hmagmaR/json (API)

# Install 'hmagmaR' in R:

install.packages('hmagmaR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aydanasg/hmagmar/issues

Datasets:

annotated_genes - Example microglia PLAC-seq dataset
enhancerRegions - Example microglia PLAC-seq dataset
gwas - Example microglia PLAC-seq dataset
hic - Example microglia PLAC-seq dataset
promoterRegions - Example microglia PLAC-seq dataset
regulatoryRegions - Example microglia PLAC-seq dataset
snpgeneexon - Example microglia PLAC-seq dataset
snps - Example microglia PLAC-seq dataset

On CRAN:

software epigenetics chipseq generegulation snp genomeannotation functionalgenomics genetarget hic

2.70 score 3 exports 146 dependencies

Last updated from:22147490bb. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	250
linux-devel	NOTE	474
source / vignettes	OK	380
linux-release	NOTE	432
macos-release	NOTE	368
macos-oldrel	NOTE	378
windows-devel	NOTE	337
windows-release	NOTE	371
windows-oldrel	NOTE	375
wasm-release	OK	214

Exports:AnnotationFileHmagma GeneLevelAnalysis_hmagma SampledDownAnnotation

Dependencies:AnnotationDbi ape aplot askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot bslib cachem caTools ChIPseeker cigarillo cli cluster codetools cpp11 crayon curl DBI digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim gplots gridGraphics gson gtable gtools highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme openssl org.Hs.eg.db patchwork pillar pkgconfig plotrix plyr png polyclip purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Vectors S7 sass scales scatterpie Seqinfo snow stringi stringr sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr TxDb.Hsapiens.UCSC.hg19.knownGene UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml yulab.utils

Introduction to hmagmaR

Rendered fromhmagmaR.Rmdusingknitr::rmarkdown

Last update: 2026-08-11
Started: 2026-08-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Gene level analysis carried out by magma (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004219)	AnnotationFileHmagma
Gene level analysis carried out by magma (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004219)	GeneLevelAnalysis_hmagma
Gene level analysis carried out by magma (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004219)	SampledDownAnnotation
Example microglia PLAC-seq dataset	annotated_genes enhancerRegions gwas hic promoterRegions regulatoryRegions snpgeneexon snps test_dataset.microglia.hg19