{ "_id": "6a1e962b1d7bb097a0a6c217", "Package": "SNPhood", "Title": "SNPhood: Investigate, quantify and visualise the epigenomic\nneighbourhood of SNPs using NGS data", "Version": "1.43.0", "Authors@R": "c(person(\"Christian\", \"Arnold\", email =\n\"christian.arnold@embl.de\", role = c(\"cre\",\"aut\")),\nperson(\"Pooja\", \"Bhat\", email = \"pooja.bhat@embl.de\", role =\n\"aut\"), person(\"Judith\", \"Zaugg\", email =\n\"judith.zaugg@embl.de\", role = \"aut\"))", "Author": "Christian Arnold [aut, cre], Pooja Bhat [aut], Judith Zaugg\n[aut]", "Maintainer": "Christian Arnold ", "Description": "To date, thousands of single nucleotide polymorphisms\n(SNPs) have been found to be associated with complex traits and\ndiseases. However, the vast majority of these\ndisease-associated SNPs lie in the non-coding part of the\ngenome, and are likely to affect regulatory elements, such as\nenhancers and promoters, rather than function of a protein.\nThus, to understand the molecular mechanisms underlying genetic\ntraits and diseases, it becomes increasingly important to study\nthe effect of a SNP on nearby molecular traits such as\nchromatin environment or transcription factor (TF) binding.\nTowards this aim, we developed SNPhood, a user-friendly\n*Bioconductor* R package to investigate and visualize the local\nneighborhood of a set of SNPs of interest for NGS data such as\nchromatin marks or transcription factor binding sites from\nChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of\neasy-to-use functions to extract, normalize and summarize reads\nfor a genomic region, perform various data quality checks,\nnormalize read counts using additional input files, and to\ncluster and visualize the regions according to the binding\npattern. The regions around each SNP can be binned in a\nuser-defined fashion to allow for analysis of very broad\npatterns as well as a detailed investigation of specific\nbinding shapes. Furthermore, SNPhood supports the integration\nwith genotype information to investigate and visualize\ngenotype-specific binding patterns. Finally, SNPhood can be\nemployed for determining, investigating, and visualizing\nallele-specific binding patterns around the SNPs of interest.", "VignetteBuilder": "knitr", "biocViews": "Software", "License": "LGPL (>= 3)", "LazyData": "true", "URL": "https://bioconductor.org/packages/SNPhood", "BugReports": "mailto:", "RoxygenNote": "5.0.1", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:05 UTC", "RemoteUrl": "https://github.com/bioc/SNPhood", "RemoteRef": "HEAD", "RemoteSha": "24cfef578f1456237d9ffd170e52bb480ad0f987", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 08:23:13 UTC", "User": "root" }, "MD5sum": "9016127b837532e90b29b378e2aacfd3", "_user": "bioc", "_type": "src", "_file": "SNPhood_1.43.0.tar.gz", "_fileid": "6d224493c0ee368c564ebcf15b4a3fb11a0af8171b61146972411ef0a0468bbe", "_filesize": 6863725, 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"topics": [ "annotationBins2" ] }, { "page": "annotationDatasets", "title": "Get the annotation(names) of the datasets in a _SNPhood_ object.", "topics": [ "annotationDatasets" ] }, { "page": "annotationReadGroups", "title": "Get the annotation(names) of the read groups in a _SNPhood_ object.", "topics": [ "annotationReadGroups" ] }, { "page": "annotationRegions", "title": "Get the annotation of SNP regions for a _SNPhood_ object.", "topics": [ "annotationRegions" ] }, { "page": "associateGenotypes", "title": "Associate genotypes with user regions from a _SNPhood_ object.", "topics": [ "associateGenotypes" ] }, { "page": "changeObjectIntegrityChecking", "title": "Disable object integrity checking for a _SNPhood_ object.", "topics": [ "changeObjectIntegrityChecking" ] }, { "page": "collectFiles", "title": "Helper function to generate a data frame that can be used as input for the function _analyzeSNPhood_", "topics": [ "collectFiles" ] }, { "page": "convertToAllelicFractions", "title": "Convert read counts across read groups to relative fractions from a _SNPhood_ object.", "topics": [ "convertToAllelicFractions" ] }, { "page": "counts-method", "title": "Extract count data from a 'SNPhood' object.", "topics": [ "counts", "counts,SNPhood-method" ] }, { "page": "deleteDatasets", "title": "Delete a particular set of datasets from a _SNPhood_ object.", "topics": [ "deleteDatasets" ] }, { "page": "deleteReadGroups", "title": "Delete a particular set of read groups.", "topics": [ "deleteReadGroups" ] }, { "page": "deleteRegions", "title": "Delete a set of user regions from a _SNPhood_ object.", "topics": [ "deleteRegions" ] }, { "page": "enrichment-methods", "title": "Extract enrichment data from an object.", "topics": [ "enrichment", "enrichment,SNPhood-method" ] }, { "page": "getDefaultParameterList", "title": "Helper function to generate a default parameter list as input for the function _analyzeSNPhood_", "topics": [ "getDefaultParameterList" ] }, { "page": "mergeReadGroups", "title": "Merges the counts of all read groups for a _SNPhood_ object", "topics": [ "mergeReadGroups" ] }, { "page": "bins-methods", "title": "Get the number of bins for a _SNPhood_ object.", "topics": [ "bins", "nBins" ] }, { "page": "datasets-methods", "title": "Get the number of datasets for a _SNPhood_ object.", "topics": [ "datasets", "nDatasets" ] }, { "page": "readGroups-methods", "title": "Get the number of read groups for a _SNPhood_ object.", "topics": [ "nReadGroups", "readGroups" ] }, { "page": "regions-methods", "title": "Get the number of SNP regions for a _SNPhood_ object.", "topics": [ "nRegions", "regions" ] }, { "page": "parameters-methods", "title": "Retrieve the parameters of an object.", "topics": [ "parameters", "parameters,SNPhood-method" ] }, { "page": "plotAllelicBiasResults", "title": "Graphically summarize the results of the allelic bias analysis for a specific dataset and region.", "topics": [ "plotAllelicBiasResults" ] }, { "page": "plotAllelicBiasResultsOverview", "title": "Visualize the results of the allelic bias analysis across regions or a user-defined genomic range", "topics": [ "plotAllelicBiasResultsOverview" ] }, { "page": "plotAndCalculateCorrelationDatasets", "title": "Calculate and plot correlation of region read counts among pairs of input files.", "topics": [ "plotAndCalculateCorrelationDatasets" ] }, { "page": "plotAndCalculateWeakAndStrongGenotype", "title": "Visualizes and calculates strong and weak genotypes.", "topics": [ "plotAndCalculateWeakAndStrongGenotype" ] }, { "page": "plotAndClusterMatrix", "title": "Clustering of read counts or enrichmens across bins for a specific dataset and read group", "topics": [ "plotAndClusterMatrix" ] }, { "page": "plotAndSummarizeAllelicBiasTest", "title": "Summarize the allelic bias analysis across SNP regions and bins and visualize some of the results.", "topics": [ "plotAndSummarizeAllelicBiasTest" ] }, { "page": "plotBinCounts", "title": "Visualize counts 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