Tools developed by BIIT research group that make use of g:Profiler services

• ClustVis is a web tool for visualizing clustering of multivariate data and uses g:Convert tool for identifier conversions.
• FuncExplorer gene clustering service based on enrichment analysis uses g:Profiler’s g:GOSt and g:Convert functions
• GOsummaries is an R package that produces word cloud summaries of GO enrichment analysis and uses gProfileR R package for that.
• GraphWeb is a web tool that allows users to apply graph algorithms on their data. It makes use of g:Orth service for orthologous gene mappings, g:Convert for identifier conversions and g:GOSt for enrichment analysis
• KEGGanim is a web tool that maps user provided high-throughput data to KEGG pathway maps and relies on g:Convert identifier conversion service.
• MEM global gene expression similarity searching tool uses g:Profiler enrichment analysis visualisation through BioJS application and g:Convert service for identifier conversions
• PAWER is protein array exploring web service that benefits from g:Convert identifier conversions and g:GOSt enrichment service.

External tools that make use of g:Profiler services

• BEHST - analyses genomic regions that intersect in 3D space according to Hi-C datasets and uses g:Profiler to list the most significant Gene Ontology terms for such interacting genes.
• UniHI - a database for retrieval, analysis and visualization of human molecular interaction networks that uses g:Convert for gene and protein name mappings.
• bulkAnalyseR - An accessible, interactive pipeline for analysing and sharing bulk sequencing results
• km2gcn - Optimization process of WGCNA hierarchical clustering with k-means
• cdgprofilergenestoterm - This repository creates a CDAPS compatible functional enrichment Docker image using gProfiler
• Enrichment Table App for Cytoscape - provides the functionality of functional enrichment analysis for any network loaded into Cytoscape
• hpgltools - A bunch of R functions to make playing with high throughput data easier
• artMS - Analytical R Tools for Mass Spectrometry
• mudi - A collection of python-based single-cell utilities and pipelines.
• piClusterBusteR - perform piRNA cluster characterization and annotation
• network_bio_toolkit - toolbox of network biology methods
• scTyper - comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
• DoriTool - bioinformatics integrative tool for post-association functional annotation
• GOMCL - tool to cluster and extract summarized associations of Gene Ontology based functions in omics data.
• scMappR - suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes
• dgeAnalysis - R-Shiny application developed to perform differential gene expression analysis
• genomeSidekick - an epigenomic data analysis application
• FunVarA - Systematic Pipeline to Unravel the Convergence Patterns of Genetic Variants in Complex Diseases
• GeneCloudOmics - web server for transcriptome data analysis and visualization
• MetaNetwork - Network analysis and visualization of proteomics data using weighted gene correlation network analysis