Package: SNPhood 1.35.0

Christian Arnold

SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

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.

Authors:Christian Arnold [aut, cre], Pooja Bhat [aut], Judith Zaugg [aut]

SNPhood_1.35.0.tar.gz
SNPhood_1.35.0.zip(r-4.5)SNPhood_1.35.0.zip(r-4.4)SNPhood_1.35.0.zip(r-4.3)
SNPhood_1.35.0.tgz(r-4.4-any)SNPhood_1.35.0.tgz(r-4.3-any)
SNPhood_1.35.0.tar.gz(r-4.5-noble)SNPhood_1.35.0.tar.gz(r-4.4-noble)
SNPhood_1.35.0.tgz(r-4.4-emscripten)SNPhood_1.35.0.tgz(r-4.3-emscripten)
SNPhood.pdf |SNPhood.html✨
SNPhood/json (API)
NEWS

# Install 'SNPhood' in R:
install.packages('SNPhood', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:SNPhood-1.35.0(bioc 3.20)SNPhood-1.34.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

41 exports 0.71 score 102 dependencies 2 mentions

Last updated 2 months agofrom:147ba412f8

Exports:analyzeSNPhoodannotationannotationBinsannotationBins2annotationDatasetsannotationReadGroupsannotationRegionsassociateGenotypeschangeObjectIntegrityCheckingcollectFilesconvertToAllelicFractionscountsdeleteDatasetsdeleteReadGroupsdeleteRegionsenrichmentgetDefaultParameterListmergeReadGroupsnBinsnDatasetsnReadGroupsnRegionsparametersplotAllelicBiasResultsplotAllelicBiasResultsOverviewplotAndCalculateCorrelationDatasetsplotAndCalculateWeakAndStrongGenotypeplotAndClusterMatrixplotAndSummarizeAllelicBiasTestplotBinCountsplotClusterAverageplotFDRResultsplotGenotypesPerClusterplotGenotypesPerSNPplotRegionCountsrenameBinsrenameDatasetsrenameReadGroupsrenameRegionsresultstestForAllelicBiases

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDESeq2fansifarverfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngR6RColorBrewerRcppRcppArmadilloRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc

Introduction and Methodological Details

Christian Arnold, Pooja Bhat, Judith Zaugg

Rendered fromIntroductionToSNPhood.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2016-03-10
Started: 2015-10-07

Workflow example

Christian Arnold, Pooja Bhat, Judith Zaugg

Rendered fromworkflow.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2017-08-11
Started: 2015-10-07

Readme and manuals

Help Manual

Help pageTopics
Main function of _SNPhood_analyzeSNPhood
Retrieve the annotation of a 'SNPhood' object.annotation annotation,SNPhood-method
Get the annotation(names) of the bins in a _SNPhood_ object.annotationBins
Get the annotation(names) of bins in a _SNPhood_ object.annotationBins2
Get the annotation(names) of the datasets in a _SNPhood_ object.annotationDatasets
Get the annotation(names) of the read groups in a _SNPhood_ object.annotationReadGroups
Get the annotation of SNP regions for a _SNPhood_ object.annotationRegions
Associate genotypes with user regions from a _SNPhood_ object.associateGenotypes
Disable object integrity checking for a _SNPhood_ object.changeObjectIntegrityChecking
Helper function to generate a data frame that can be used as input for the function _analyzeSNPhood_collectFiles
Convert read counts across read groups to relative fractions from a _SNPhood_ object.convertToAllelicFractions
Extract count data from a 'SNPhood' object.counts counts,SNPhood-method
Delete a particular set of datasets from a _SNPhood_ object.deleteDatasets
Delete a particular set of read groups.deleteReadGroups
Delete a set of user regions from a _SNPhood_ object.deleteRegions
Extract enrichment data from an object.enrichment enrichment,SNPhood-method
Helper function to generate a default parameter list as input for the function _analyzeSNPhood_getDefaultParameterList
Merges the counts of all read groups for a _SNPhood_ objectmergeReadGroups
Get the number of bins for a _SNPhood_ object.bins nBins
Get the number of datasets for a _SNPhood_ object.datasets nDatasets
Get the number of read groups for a _SNPhood_ object.nReadGroups readGroups
Get the number of SNP regions for a _SNPhood_ object.nRegions regions
Retrieve the parameters of an object.parameters parameters,SNPhood-method
Graphically summarize the results of the allelic bias analysis for a specific dataset and region.plotAllelicBiasResults
Visualize the results of the allelic bias analysis across regions or a user-defined genomic rangeplotAllelicBiasResultsOverview
Calculate and plot correlation of region read counts among pairs of input files.plotAndCalculateCorrelationDatasets
Visualizes and calculates strong and weak genotypes.plotAndCalculateWeakAndStrongGenotype
Clustering of read counts or enrichmens across bins for a specific dataset and read groupplotAndClusterMatrix
Summarize the allelic bias analysis across SNP regions and bins and visualize some of the results.plotAndSummarizeAllelicBiasTest
Visualize counts or enrichment for a particular region across bins, datasets, and read groups.plotBinCounts
Visualize average enrichment per clusterplotClusterAverage
Graphically summarize the results of the allelic bias analysis for a specific dataset and region.plotFDRResults
Visualize average counts/enrichment based on strong and weak genotypes.plotGenotypesPerCluster
Plot genotype frequencies of regions across datasets.plotGenotypesPerSNP
Visualize the raw read counts across regions or a user-defined genomic rangeplotRegionCounts
Rename bins.renameBins
Rename datasets.renameDatasets
Rename read groups.renameReadGroups
Rename regions.renameRegions
Get results of various analyses performed with a 'SNPhood' object.results
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS dataSNPhood-package SNPhood
A class to represent, investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS dataSNPhood-class
SNPhood example dataSNPhood-data SNPhood.o
Perform an allelic bias tests for each user region and bin.testForAllelicBiases