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gprofiler2: Interface to the ‘g:Profiler’ Toolset

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Package ‘gprofiler2’ August 23, 2021 Type Package Title Interface to the ‘g:Profiler’ Toolset Version 0,2,1 Author Liis Kolberg , Uku Raudvere

Gene list functional enrichment analysis and namespace

Gene list functional enrichment analysis and namespace conversion with gprofiler2,

g:Profiler – a web server for functional enrichment

Installation, gprofiler2 can be installed from CRAN install,packages”gprofiler2“or via conda from the conda-forge channel conda install -c conda-forge r-gprofiler2

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g:Profiler – a web server for functional enrichment

g:GOSt performs functional enrichment analysis, also known as over-representation analysis ORA or gene set enrichment analysis, on input gene list, It maps genes to known functional information sources and detects statistically significantly enriched terms, We regularly retrieve data from Ensembl database and fungi, plants or metazoa specific

gprofiler-official, PyPI

gprofiler Project description, The official Python 3 interface to the g:Profiler toolkit for enrichment analysis of functional GO and other terms, conversion between identifier namespaces and mapping orhologous genes in related organisms,, It has an optional dependency on pandas, Installing gprofiler, the recommended way of installing gprofiler is using pip

g:Profiler – a web server for functional enrichment

g:GOSt performs functional enrichment analysis, also known as over-representation analysis ORA or gene set enrichment analysis, on input gene list, It maps genes to known functional information sources and detects statistically significantly enriched terms, We regularly retrieve data from Ensembl database and fungi, plants or metazoa specific versions of Ensembl Genomes, and parasite

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Profiler — Wikipédia

Synopsis

gprofiler2 — an R package for gene list functional

As the gprofiler2 R package and the web tool are in sync, this token will also work for the analysis in the web tool and can be inserted under the section “Bring your own data Custom GMT”, And vice versa, the token obtained from the web tool will work in the R package without uploading the data again, Thus, in order to analyse multiple gene lists with the same data source, the user needs

g:Profiler: a web server for functional enrichment

Introduction

gprofiler2: vignettes/gprofiler2,Rmd

gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool, The list of organisms and corresponding data sources is available here, The full list of namespaces that g:Profiler recognizes is available here, Citation, If you use the R package gprofiler2 in published research, please cite: Kolberg, L,, Raudvere, U,, Kuzmin, I,, Vilo, J, and Peterson, H,, 2020

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