Package: SNPannotator 1.4.8

Alireza Ani

SNPannotator: Automated Functional Annotation of Genetic Variants and Linked Proxies

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.

Authors:Alireza Ani [aut, cre], Zoha Kamali [aut], Ahmad Vaez [aut]

SNPannotator_1.4.8.tar.gz
SNPannotator_1.4.8.tar.gz(r-4.7-any)SNPannotator_1.4.8.tar.gz(r-4.6-any)
SNPannotator_1.4.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SNPannotator/json (API)

# Install 'SNPannotator' in R:

install.packages('SNPannotator', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

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

2.70 score 3 scripts 535 downloads 13 exports 92 dependencies

Last updated from:e43674890a. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	252
source / vignettes	OK	214
linux-release-x86_64	OK	247
wasm-release	OK	165

Exports:annotate_shiny demo_annotation EnsemblDatabases EnsemblReleases findGenomicPos findPairwiseLD findProxy findRSID findSynonyms getConfigFile merge_annotations run_annotation run_stringdb_annotation

Dependencies:askpass base64enc bit bit64 bslib cachem cli clipr cpp11 crayon curl data.table digest dplyr evaluate farver fastmap fontawesome fs generics ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable highr hms htmltools httr igraph ini isoband jquerylib jsonlite kableExtra knitr labeling lattice lifecycle logger magrittr MASS Matrix memoise mime openssl openxlsx pillar pkgconfig png polyclip prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr rlang rmarkdown rstudioapi S7 sass scales stringi stringr svglite sys systemfonts textshaping tibble tidygraph tidyr tidyselect tinytex tweenr tzdb utf8 vctrs viridis viridisLite vroom withr xfun xml2 yaml zip

Introduction to SNPannotator package

Rendered fromSNPannotator-intro.Rmdusingknitr::rmarkdown

Last update: 2025-11-26
Started: 2025-11-16

Citation

Readme and manuals

Help Manual

Help page	Topics
Run the annotation pipeline on a list of variants from shiny app	annotate_shiny
Demo run of the annotation pipeline	demo_annotation
List population from human database (1000 Genomes project)	EnsemblDatabases
data release available on this REST server.	EnsemblReleases
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.	findGenomicPos
Computes and returns LD values between the given variants.	findPairwiseLD
Finds variants in high LD	findProxy
Query Ensembl for variant information based on genomic position	findRSID
Find variant synonyms from Ensembl	findSynonyms
Copy a sample configuration file	getConfigFile
Merge multiple inSilico annotation output objects and export to Excel	merge_annotations
Checks if the service is alive	pingEnsembl
Run the annotation pipeline on a list of variants	run_annotation
Analyze STRING DB Interactions and perform functional enrichment	run_stringdb_annotation

Package: SNPannotator 1.4.8

SNPannotator: Automated Functional Annotation of Genetic Variants and Linked Proxies

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)