SNPannotator (version 1.4.3)

Automated Functional Annotation of Genetic Variants and Linked Proxies

Description

To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.

Copy Link

Version

Install

install.packages('SNPannotator')

Monthly Downloads

552

Version

1.4.3

License

GPL-3

Maintainer

Alireza Ani

Last Published

November 26th, 2025

Functions in SNPannotator (1.4.3)

annotate_shiny

Run the annotation pipeline on a list of variants from shiny app

demo_annotation

Demo run of the annotation pipeline

findPairwiseLD

Computes and returns LD values between the given variants.

mergeResultFiles

Merge multiple output files

EnsemblReleases

data release available on this REST server.

getConfigFile

Copy a sample configuration file

findProxy

Finds variants in high LD

findGenomicPos

Query GTEx portal for Variant's genomic position based on rsID Retrieves variant information from the GTEx portal using either an rsID or a variant ID formatted as CHR_POS_REF_ALT. If an rsID is provided, the function returns the corresponding genomic positions in both GRCh37 and GRCh38 builds. When searching for an rsID based on genomic position, the position parameter should be specified according to the GRCh38 reference genome.

findRSID

Query Ensembl for variant information based on genomic position

EnsemblDatabases

List population from human database (1000 Genomes project)

run_stringdb_annotation

Analyze STRING DB Interactions and perform functional enrichment

pingEnsembl

Checks if the service is alive

run_annotation

Run the annotation pipeline on a list of variants