Welcome to the new bioconductor.org!

SNPhood

This is the development version of SNPhood; for the stable release version, see SNPhood.

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


Bioconductor version: Development (3.19)

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.

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

Maintainer: Christian Arnold <christian.arnold at embl.de>

Citation (from within R, enter citation("SNPhood")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SNPhood")

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("SNPhood")
Introduction and Methodological Details HTML R Script
Workflow example HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Software
Version 1.33.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License LGPL (>= 3)
Depends R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate
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
System Requirements
URL https://bioconductor.org/packages/SNPhood
Bug Reports mailto:
See More
Suggests BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
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 SNPhood_1.33.0.tar.gz
Windows Binary SNPhood_1.33.0.zip
macOS Binary (x86_64) SNPhood_1.33.0.tgz
macOS Binary (arm64) SNPhood_1.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SNPhood
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SNPhood
Bioc Package Browser https://code.bioconductor.org/browse/SNPhood/
Package Short Url https://bioconductor.org/packages/SNPhood/
Package Downloads Report Download Stats