Actively maintained software
- g:Profiler – functional profiling of gene lists from large scale experiments (article)
- MEM (Multi Experiment Matrix) – large-scale gene expression data queries and mining (article)
- ClustVis – a web tool for visualizing clustering of multivariate data (article)
- funcExplorer– a web tool that extracts the most significant biological features of a dataset using clustering combined with functional annotations
- KEGGanim – animation of pathways using high-throughput data (article)
- GraphWeb – a tool for mining large biological networks (article)
- DosOpt – a web-based tool for Bayesian dose adjustment during clinical treatment (article)
- MethSurv – a web tool to perform multivariable survival analysis using DNA methylation data (article)
- PAWER – ProtoArray Web ExploreR is a tool for analysing protein microarray data (Protoarrays)
- EDAMmap – tool for mapping text to bioinformatics ontology EDAM. It is designed to assist a curator annotate tools and services in the field of bioinformatics.
- The Virtual Coffee Room – Questions and answers forum dedicated for communication related to ELIXIR
- gprofiler2 – the new R interface for the g:Profiler web service
- gProfileR – the old R interface for the g:Profiler web service
- wiggleplotr – Make read coverage plots from BigWig files
- pheatmap – Pretty heatmaps
- GOsummaries – Word cloud summaries of Gene Ontology enrichment analysis (article)
- RobustRankAggreg – Methods for robust rank aggregation
- seqlm – an MDL based method for identifying differentially methylated regions in high density methylation array data
Information retrieval related algorithms and data structures
- Search of Russian words in latin alphabet (Estonian); old Estonian words; etc based on universal edit distance engine
- Search of English words based on pronunciation (in Estonian)
- Generalized edit distance command line tool (Reina Uba; Siim Orasmaa) allows to find approximate matches between a search string and list of strings in a dictionary. In addition to the regular edit distance (the Levenshtein distance), a set of weighted transformations can be used in a search.
- Very fast approximate regular expression matching using shift-OR based automaton matching.
This software is no longer actively maintained.
- ESCD – Embryonic Stem Cell Database (article)
- FunGenES Data Atlas – A Genomics Resource for Mouse Embryonic Stem Cell Differentiation (article)
- m:Explorer – identifying process-specific gene regulators from high-throughput genomic data (article)
- G=MAT: Linking Transcription Factor Expression with DNA Binding
- HappieClust – Fast approximate hierarchical clustering using similarity heuristics (article)
- SWOG – Simple Web Object Graphics