Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free
Documentation
R

gprofiler2

Interface to the 'g:Profiler' Toolset

A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>). The main tools are: (1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists; (2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces; (3) 'g:Orth' - orthology search across species; (4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.

Functions (16)

gconvert

Gene ID conversion.

get_base_url

Get the current base URL.

get_tls_version

Get the TLS version for SSL

get_user_agent

Get current user agent string.

gorth

Orthology search.

gost

Gene list functional enrichment.

gostplot

Manhattan plot of functional enrichment results.

gsnpense

Convert SNP rs identifiers to genes.

mapViridis

Map vector of numeric values to Viridis color scale.

publish_gostplot

Create and save an annotated Manhattan plot of enrichment results.

publish_gosttable

Create and save a table with the functional enrichment analysis results.

random_query

Generate a random gene list for testing.

set_base_url

Set the base URL.

set_tls_version

Set the TLS version to use for SSL

set_user_agent

Set custom user agent string.

upload_GMT_file

Upload custom annotations for functional enrichment analysis in g:GOSt.

gprofiler2

Interface to the 'g:Profiler' Toolset

v0.2.0
GPL (>= 2)
Authors
Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Initial release

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.