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 (3.18)
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("SNPhood")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | Software |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8 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 |
| Linking To | |
| Suggests | BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot |
| System Requirements | |
| Enhances | |
| URL | https://bioconductor.org/packages/SNPhood |
| Bug Reports | mailto: |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SNPhood_1.31.0.tar.gz |
| Windows Binary | SNPhood_1.31.0.zip |
| macOS Binary (x86_64) | SNPhood_1.31.0.tgz |
| macOS Binary (arm64) | |
| 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 |