Services: software tools

Tool for prediction of disease related mutations in proteins. Tool version 2 (PredictSNP 2) for prediction of disease related mutatins within human genome available since 2016.

Primer3 is a program for designing PCR primers and oligos. 

Tool for the detection of structurally similar protein binding sites and pairwise local structural alignment

PROGENy provides a function to infer pathway activity from gene expression. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signalling footprints in cancer gene expression

A complete, flexible analysis of protein microarrays for biomarker discovery. Part of the Proteomics Toolbox. 

An algorithm suite combining Protein Spectrum Matches from different experiments / search engines for consistent, comparable results. Part of the Proteomics Toolbox. 

ProteoSign: an end-user online differential proteomics statistical analysis platform

A software tool for the identification of common transcription factors that are likely to regulate a user defined set of genes. PscanChIP is the extension of Pscan to process ChIP-Seq enriched regions.

The PSIPRED Protein Structure Analysis Workbench aggregates several UCL Bioinformatics Group prediction methods into one location. 

A PyMOL plugin, designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools.

Webtool for automated quality control and statistical analysis of protein expression following labelled mass spectrometry experiments

Importing and analysing Mass Spec. data in a range of formats and for protein identification.
 

RNA-Seq Analysis Pipeline

A cloud computing web application implementing a complete and modular RNA-Seq analysis workflow.

A tool for analyzing BLAST search output for RNA sequences.

Exploring and evaluating NGS data utilizing a modular programming structure allowing easy plugins.

A transcriptome-based breast tumor diagnostic tool

Python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

Set of tools and a web server for complex characterization of repetitive DNA based on data from next generation of sequence reads.

The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.

rGreat is an R package which acts as a client of GREAT enrichment analysis analysis

The rhdf5 and Rhdf5lib packages combine to provide an interface between HDF5 and R. The HDF5 file format provides the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) in a completely portable manner. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
In particular HDF5 is being used to address the rapid growth in the size of single-cell datasets, and rhdf5 is a cornerstone to many existing analysis tools.

A web portal dedicated to ribosome profiling (RiboSeq) data analysis. There are currently two resources with Tutorial support and a Forum for both.

Residue interaction network generator. RING identifies all types of non-covalent interactions at atomic level in a protein structure (PDB);

Providing access to many NGS and RNA tools, visualisations, interactive environments (e.g. IPython) as well as various utilities, reference genomes and data libraries.

End-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. Starting from the FASTQ files are aligned to the reference genome, and a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample is prepared. Performance of exploratory data analysis (EDA) for quality assessment and exploration of the relationship between samples, performance of differential gene expression analysis, and visual exploration of the results.

Tools for packaging of research data with associated metadata. The offered packaging solutions focus on practical implementations targeting community use cases

Identification and validation of predictive biomarkers based on gene expression in solid tumors

Roddy is a framework for large scale NGS processing pipelines on Petabyte scale. It is used for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Web tool for prediction of rRNA secondary structures.

Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. The tools can be accessed via a Web site (http:rsat.eu/), as Web services, or installed locally on Linux / Mac OS X systems.