Bioconductor

biomaRtHuber Group, A bridge from R to BioMart databases - for instance Ensembl
cellHTS2Huber Group, Analysis of cell-based high-throughput screens
DESeqSteinmetz 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
DEXSeqHuber Group, Inference of differential exon usage in RNA-Seq
easyRNASeqSteinmetz Group, Count summarisation and normalisation for RNA-Seq data
EBImageHuber Group, Image processing and analysis toolkit for R
genomeIntervalsSteinmetz 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
HilbertVisHuber Group, Visualize long vectors of data by means of Hilbert curves
imageHTSHuber Group, Analysis of high-throughput microscopy-based screens
mgsaSteinmetz Group, Model-based Gene Set Analysis(MGSA), a Bayesian modelling approach for gene set enrichment
rhdf5Huber Group, HDF5 interface to R
RingoHuber Group, Analysis of ChIP-chip data
tilingArrayHuber Group, Transcript mapping with high-density oligonucleotide tiling arrays
vsnHuber Group, Normalization and variance stabilizing transformation of microarray data.
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Database

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

CopySeqKorbel Group, Discovery and copy-number genotyping of genomic structural variants
DELLYKorbel Group, Integrated split-read and paired-end based structural variant discovery in massively parallel sequencing data
HTSeqSteinmetz 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
PEMerKorbel Group, Discovery of genomic structural variants by high-throughput and massive paired-end mapping
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Gene Analysis

BLAST2GENEBork Group, Gene analysis in genomic regions
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Gene Expression

4DXpressArendt Group, A database for cross species gene expression data acquired through high-resolution in situ experiments
PEPDArendt Group,  
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Microscopy

MicropilotPepperkok 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

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

switches.ELMGibson 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.
ADANStructural 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 HarvesterPepperkok 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.
CaMKipediaGibson Team, The human CaM Kinase Encyclopedia
EpiCGibson Team, EpiC applies protein structure-function information to help identify target epitopes for antibody design
gfp-cDNAPepperkok Team, Localisation and functional characterisation of gfp-tagged novel human cDNAs
iELMGibson Team, Exploring interactions of motifs
MATADORBork Group, Manually Annotated Targets and Drugs Online Resource
Phospho.ELMGibson Team, Phospho.ELM provides a linked database of experimentally verified phosphorylation sites in eukaryotic proteins.
SMARTBork Group, Simple Modular Architecture Research Tool
SNPeffectStructural 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.
STITCHBork Group, A resource to explore known and predicted interactions of chemicals and proteins
STRINGBork Group, Search Tool for the Retrieval of Interacting Genes/Proteins
The ELM ServerGibson Team, Investigation of functional sites in protein sequences with the Eukaryotic Linear Motif database.
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Sequence Analysis

BLAST SK1/ YJM789/S288cSteinmetz Group, BLAST server for assembled genomes from S. cerevisiae strains SK1, YJM789, and S288c
BreakSeqKorbel Group, Nucleotide-resolution genotyping of structural variants in personal genomics data
TrawlerArendt Group,  
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Imaging mass spectrometry

pyimzMLAlexandrov Team, A parser to read .imzML files with Python
pyMSAlexandrov Team, Python library for mass spectrometry
pySMAlexandrov Team, Python library for spatial metabolomics
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Structural Analysis

AGADIRStructural and Computational Biology Unit, An algorithm to predict the helical content of peptides
ARP/wARPLamzin Group, Automated model building of protein structures, version 7.3
ATSASSvergun Group, A programme suite for small-angle scattering data analysis of biological macromolecules.
ATSAS-ONLINESvergun Group, A Web interface to major programmes from the ATSAS 2.2 suite for small-angle scattering data analysis from biological macromolecules.
Auto-RickshawLamzin Group, The EMBL Hamburg automated crystal structure determination platform
BESTLamzin Group, Advanced Diffraction Data Collection Strategy programme.
DisEMBLGibson Team, DisEMBL is a disorder predictor targetted at Structural Genomics Initiatives.
FOLDX: Tools for Protein DesignStructural and Computational Biology Unit, Force field for energy calculations in proteins
GlobPlotGibson Team, GlobPlot is a server for exploring disorder or globularity in protein sequences.
PolyPhenBork Group, Prediction of functional effect of human nsSNPs
RapidoSchneider (Thomas) Group, Structure superposition and identification of rigid domains
TANGOStructural and Computational Biology Unit, Software for predicting protein aggregation
ViCiLamzin Group, In-silico ligand-based drug design
Xlink AnalyzerBeck Group, An interactive software for visualising cross-links on structures and analysing how the structures agree with the cross-links.
XRECLamzin Group, Automated crystal identification and centring on a beamline goniostat, version 3.1
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Systems Biology Software

SmartCellStructural 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

LSATBork Group, Literature Support for Alternative Transcripts
XplorMedBork Group, Explore a bibliographic search in MEDLINE
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Liquid chromatography mass spectrometry

OptimusAlexandrov Team, Workflow for feature detection, quantification, filtering, and annotation for LC-MS
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Literature And Data Mining

HIV mutation browserBriggs Group, Database of mutagenesis and mutation data on HIV collected from the scientific literature
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Visualisation

HilbertVisHuber Group, Visualization of genomic data with the Hilbert curve
`iliAlexandrov Team, Google Chrome app for visualization of spatially mapped data in 2D and 3D
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Miscellaneous

BreakPtrKorbel Group, Mapping copy-number variation with high-density oligonucleotide tiling arrays.

PEMerKorbel Group, Discovery of genomic structural variants by high-throughput and massive paired-end mapping
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