Package: SNPhood
Title: SNPhood: Investigate, quantify and visualise the epigenomic
        neighbourhood of SNPs using NGS data
Version: 1.41.0
Authors@R: c(person("Christian", "Arnold", email =
        "christian.arnold@embl.de", role = c("cre","aut")),
        person("Pooja", "Bhat", email = "pooja.bhat@embl.de", role =
        "aut"), person("Judith", "Zaugg", email =
        "judith.zaugg@embl.de", role = "aut"))
Author: Christian Arnold [aut, cre], Pooja Bhat [aut], Judith Zaugg
        [aut]
Maintainer: Christian Arnold <christian.arnold@embl.de>
Description: To date, thousands of single nucleotide polymorphisms
        (SNPs) have been found to be associated with complex traits and
        diseases. However, the vast majority of these
        disease-associated SNPs lie in the non-coding part of the
        genome, and are likely to affect regulatory elements, such as
        enhancers and promoters, rather than function of a protein.
        Thus, to understand the molecular mechanisms underlying genetic
        traits and diseases, it becomes increasingly important to study
        the effect of a SNP on nearby molecular traits such as
        chromatin environment or transcription factor (TF) binding.
        Towards this aim, we developed SNPhood, a user-friendly
        *Bioconductor* R package to investigate and visualize the local
        neighborhood of a set of SNPs of interest for NGS data such as
        chromatin marks or transcription factor binding sites from
        ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of
        easy-to-use functions to extract, normalize and summarize reads
        for a genomic region, perform various data quality checks,
        normalize read counts using additional input files, and to
        cluster and visualize the regions according to the binding
        pattern. The regions around each SNP can be binned in a
        user-defined fashion to allow for analysis of very broad
        patterns as well as a detailed investigation of specific
        binding shapes. Furthermore, SNPhood supports the integration
        with genotype information to investigate and visualize
        genotype-specific binding patterns. Finally, SNPhood can be
        employed for determining, investigating, and visualizing
        allele-specific binding patterns around the SNPs of interest.
Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8),
        BiocParallel, VariantAnnotation, BiocGenerics, IRanges,
        methods, SummarizedExperiment, RColorBrewer, Biostrings,
        grDevices, gridExtra, stats, grid, utils, reshape2, scales,
        S4Vectors
Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate
Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
VignetteBuilder: knitr
biocViews: Software
License: LGPL (>= 3)
LazyData: true
URL: https://bioconductor.org/packages/SNPhood
BugReports: mailto:<christian.arnold@embl.de>
RoxygenNote: 5.0.1
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:28:24 UTC
RemoteUrl: https://github.com/bioc/SNPhood
RemoteRef: HEAD
RemoteSha: 4de7497f50a6f251b7ee1d40ff5e1e859aab8031
NeedsCompilation: no
Packaged: 2025-10-30 11:30:22 UTC; root
Built: R 4.6.0; ; 2025-10-30 11:33:47 UTC; windows
