| biomaRt | Huber Group, A bridge from R to BioMart databases – for instance Ensembl |
| cellHTS2 | Huber Group, Analysis of cell-based high-throughput screens |
| DESeq | Steinmetz Group, Testing for differential expression in RNA-Seq and other count data |
| Huber Group, Testing for differential expression in RNA-Seq and other count data | |
| DEXSeq | Huber Group, Inference of differential exon usage in RNA-Seq |
| easyRNASeq | Steinmetz Group, Count summarisation and normalisation for RNA-Seq data |
| EBImage | Huber Group, Image processing and analysis toolkit for R |
| genomeIntervals | Steinmetz Group, Operations on genomic intervals such as merging, overlap detection, or computing distances between intervals |
| Huber Group, Operations on genomic intervals such as merging, overlap detection, or computing distances between intervals | |
| HilbertVis | Huber Group, Visualize long vectors of data by means of Hilbert curves |
| imageHTS | Huber Group, Analysis of high-throughput microscopy-based screens |
| mgsa | Steinmetz Group, Model-based Gene Set Analysis(MGSA), a Bayesian modelling approach for gene set enrichment |
| rhdf5 | Huber Group, HDF5 interface to R |
| Ringo | Huber Group, Analysis of ChIP-chip data |
| tilingArray | Huber Group, Transcript mapping with high-density oligonucleotide tiling arrays |
| vsn | Huber Group, Normalization and variance stabilizing transformation of microarray data. |
| Chaetomium thermophilum genome resource | Bork Group, The first complete genome of a true thermophilic eukaryote |
| Companion website | Bork Group, Companion website for TaraOcean’s paper: Sunagawa, Coelho, Chaffron, et al. (2015) Structure and function of the global ocean microbiome, Science, doi:10.1126/science.1261359. List of available yeast strains expressing a tagged-protein fusion. |
| EMBL Nucleotide Sequence Database | Web Production, The EMBL Nucleotide Sequence Database constitutes Europe’s primary nucleotide sequence resource. |
| Membrane-recruitment principle for PH domains | Gavin Group (Visiting), Supplementary data for the manuscript: Vonkova, I, Saliba, A.E., Deghou, S et al. (2015) Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains, Cell Reports, doi:10.1016/j.celrep.2015.07.054. |
| Suppl. to variablecomplexes | Bork Group, Protein complex stoichiometry |
| Yeast protein complexes | Gavin Group (Visiting), Database for the manuscript: Gavin, A.C., Aloy, P. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery, Nature, doi:10.1038/nature04532. List of available yeast strains expressing a tagged-protein fusion. |
| CopySeq | Korbel Group, Discovery and copy-number genotyping of genomic structural variants |
| DELLY | Korbel Group, Integrated split-read and paired-end based structural variant discovery in massively parallel sequencing data |
| HTSeq | Steinmetz Group, A Python package for processing and analysing data from high-throughput sequencing assays |
| Huber Group, A Python package for processing and analysing data from high-throughput sequencing assays | |
| PEMer | Korbel Group, Discovery of genomic structural variants by high-throughput and massive paired-end mapping |
| 4DXpress | Arendt Group, A database for cross species gene expression data acquired through high-resolution in situ experiments |
| PEPD | Arendt Group, This database contains gene expression data of Platynereis dumerilii examined through whole mount in situ hybridization |
| PTMcode | Bork Group, A resource for functional associations of post-translational modifications within and between proteins |
| Liposome microarray-based assay (LiMA) protocols | Gavin Group (Visiting), Bioinformatics tools for LiMA data analysis: Saliba, A.E., Vonkova, I, et al. (2014) A quantitative liposome microarray to systematically characterize protein-lipid interactions, Nature Methods, doi:10.1038/nmeth.2734. |
| Micropilot | Pepperkok Team, Micropilot is a microscopy software that can be rapidly trained to automatically identify cells of interest. |
| Advanced Light Microscopy Facility, Micropilot is a microscopy software that can be rapidly trained to automatically identify cells of interest. | |
| Ellenberg Group, Micropilot is a microscopy software that can be rapidly trained to automatically identify cells of interest. |
| eggNOG | Bork Group, Evolutionary genealogy of genes: Non-supervised Orthologous Groups |
| ETE 3 | Bork Group, Reconstruction, Analysis, and Visualization of Phylogenomic Data |
| iTOL | Bork Group, Interactive Tree Of Life – an online tool for the display and manipulation of phylogenetic trees |
| switches.ELM | Gibson Team, The switches.ELM resource curates experimentally validated motif-based molecular switches and predicts possible switching mechanisms that might regulate a user-submitted motif of interest. |
| ADAN | Structural and Computational Biology Unit, ADAN database offers the FOLD-X scoring matrices for ligand predictions and putative partners from protein domains when available, as well as homology models. A querying function allows the user to input a polypeptide sequence and retrieve the putative binding segments for a particular domain. |
| Bioinformatic Harvester | Pepperkok Team, The Bioinformatic Harvester collects and displays bioinformatic protein information and predictions for human proteins from various databases for realtime access. The Marvester does the same for mouse proteins. |
| CaMKipedia | Gibson Team, The human CaM Kinase Encyclopedia |
| EpiC | Gibson Team, EpiC applies protein structure-function information to help identify target epitopes for antibody design |
| gfp-cDNA | Pepperkok Team, Localisation and functional characterisation of gfp-tagged novel human cDNAs |
| iELM | Gibson Team, Exploring interactions of motifs |
| MATADOR | Bork Group, Manually Annotated Targets and Drugs Online Resource |
| Phospho.ELM | Gibson Team, Phospho.ELM provides a linked database of experimentally verified phosphorylation sites in eukaryotic proteins. |
| SMART | Bork Group, Simple Modular Architecture Research Tool |
| SNPeffect | Structural and Computational Biology Unit, SNPeffect analyses the effect of coding, non-synonymous SNPs on 3 categories of functional and physico-chemical properties of the affected proteins, namely protein structure and dynamics (stability, aggregation, dynamics, etc), integrity of functional sites and cellular processing. |
| STITCH | Bork Group, A resource to explore known and predicted interactions of chemicals and proteins |
| STRING | Bork Group, Search Tool for the Retrieval of Interacting Genes/Proteins |
| The ELM Server | Gibson Team, Investigation of functional sites in protein sequences with the Eukaryotic Linear Motif database. |
| BLAST SK1/ YJM789/S288c | Steinmetz Group, BLAST server for assembled genomes from S. cerevisiae strains SK1, YJM789, and S288c |
| BreakSeq | Korbel Group, Nucleotide-resolution genotyping of structural variants in personal genomics data |
| Trawler | Arendt Group, |
| cpyMSpec | Alexandrov Team, High performance implementations shadowing pyMSpec |
| pyImagingMSpec | Alexandrov Team, Python library for handling imaging mass spectrometry data |
| pyimzML | Alexandrov Team, A parser to read .imzML files with Python |
| pyMSpec | Alexandrov Team, Python library for mass spectrometry data |
| pySM | Alexandrov Team, Python library for metabolite annotation of imaging mass spectrometry |
| spatial-metabolomics | Alexandrov Team, Metabolite annotation engine for imaging mass spectrometry developed in the framework of the EU H2020 project METASPACE |
| AGADIR | Structural and Computational Biology Unit, An algorithm to predict the helical content of peptides |
| ARP/wARP | Lamzin Group, Automated model building of protein structures, version 7.3 |
| Assembline | Kosinski Group, Protocol for integrative structural modeling of macromolecular complexes |
| ATSAS | Svergun Group, A programme suite for small-angle scattering data analysis of biological macromolecules. |
| ATSAS-ONLINE | Svergun Group, A Web interface to major programmes from the ATSAS 2.2 suite for small-angle scattering data analysis from biological macromolecules. |
| Auto-Rickshaw | Lamzin Group, The EMBL Hamburg automated crystal structure determination platform |
| BEST | Lamzin Group, Advanced Diffraction Data Collection Strategy programme. |
| DisEMBL | Gibson Team, DisEMBL is a disorder predictor targetted at Structural Genomics Initiatives. |
| FOLDX: Tools for Protein Design | Structural and Computational Biology Unit, Force field for energy calculations in proteins |
| GlobPlot | Gibson Team, GlobPlot is a server for exploring disorder or globularity in protein sequences. |
| PolyPhen | Bork Group, Prediction of functional effect of human nsSNPs |
| Rapido | Schneider Group, Structure superposition and identification of rigid domains |
| TANGO | Structural and Computational Biology Unit, Software for predicting protein aggregation |
| ViCi | Lamzin Group, In-silico ligand-based drug design |
| Xlink Analyzer | Beck Group (Visiting), An interactive software for visualising cross-links on structures and analysing how the structures agree with the cross-links. |
| Kosinski Group, An interactive software for visualising cross-links on structures and analysing how the structures agree with the cross-links. | |
| XREC | Lamzin Group, Automated crystal identification and centring on a beamline goniostat, version 3.1 |
| SmartCell | Structural and Computational Biology Unit, A cell network simulation program supporting localisation and diffusion by using a mesoscopic stochastic reaction model. |
| curatr | Alexandrov Team, Web-app for selecting and exporting high quality tandem-ms reference spectra |
| Optimus | Alexandrov Team, Workflow for feature detection, quantification, filtering, and annotation for LC-MS |
| OptimusViewer | Alexandrov Team, An app for visualising LC-MS features |
| AGADIR | Structural and Computational Biology Unit, An algorithm to predict the helical content of peptides |
| HilbertVis | Huber Group, Visualization of genomic data with the Hilbert curve |
| iPath | Bork Group, Interactive Pathways Explorer (iPath) is a web-based tool for the visualization, analysis and customization of various pathway maps |
| ili | Alexandrov Team, Google Chrome app for visualization of spatially mapped data in 2D and 3D |
| BreakPtr | Korbel Group, Mapping copy-number variation with high-density oligonucleotide tiling arrays. |
| PEMer | Korbel Group, Discovery of genomic structural variants by high-throughput and massive paired-end mapping |