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Bioinformatics Services

Bioconductor

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
EBImage Huber Group, Image processing and analysis toolkit for R
genomeIntervals Huber Group, Operations on genomic intervals such as merging, overlap detection, or computing distances between intervals
Steinmetz 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.
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Database

EMBL Nucleotide Sequence Database EBI Web Production, The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource.
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High-throughput sequencing

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
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Gene Analysis

BLAST2GENE Bork Group, Gene analysis in genomic regions
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Gene Expression

4DXpress Arendt Group, A database for cross species gene expression data acquired through high-resolution in situ experiments
MEPD Arendt Group, A database for medaka gene expression data acquired through high-resolution in situ experiments.
PEPD Arendt Group,  
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Microscopy

Micropilot Pepperkok Team, Micropilot is a microscopy software that can be rapidly trained to automatically identify cells of interest.
Advanced Light Microscopy Core 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.
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Phylogeny

eggNOG Bork Group, Evolutionary genealogy of genes: Non-supervised Orthologous Groups
iTOL Bork Group, Interactive Tree Of Life - an online tool for the display and manipulation of phylogenetic trees
MLTreeMap Bork Group, Phylogenetic analysis of metagenomics sequence data
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Protein Function Analysis

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.
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Sequence Analysis

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,  
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Structural Analysis

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
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 (Thomas) 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
XREC Lamzin Group, Automated crystal identification and centring on a beamline goniostat, version 3.1
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Systems Biology Software

SmartCell Structural and Computational Biology Unit, A cell network simulation program supporting localisation and diffusion by using a mesoscopic stochastic reaction model.
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Text Mining

LSAT Bork Group, Literature Support for Alternative Transcripts
XplorMed Bork Group, Explore a bibliographic search in MEDLINE
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Visualization

HilbertVis Huber Group, Visualization of genomic data with the Hilbert curve
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Miscellaneous

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
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