Service list

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.

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. 

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.

RnBeads is an R package for analysing DNA methylation data obtained with an experimental protocol that provides single-CpG resolution. 

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.

A framework for software development in bioinformatics. It covers three aspects:.

1. Workflow wrapping the TF text-mining results from https://github.com/fnl plus other databases. 
2. High Throughput Sequencing related functionalities.
3. Rbbt wrapper for the Variant Effect Predictor.

Auto-downloads and installs the software.

Web interface accessing a curated database with information about biochemical reactions and kinetic properties in an experimental or environmental context.

A comprehensive data resource for salmonids species based on different omics data

A database with high-quality curated and freely accessible SARS-CoV-2 genomics- and contextual resources.

sciCORE provides a high-performance computing infrastructure, large-scale storage resources, scientific software and databases, server infrastructures and user support. It also provides expertise to scientific research groups.

Comprehensive resource of human phosphosites within their full context.

Annotation of secondary structure elements in proteins.

A tool for semantic analysis of microarray data based on a collection of workflow components for Orange4WS

For handing data that needs to be protected against unauthorized access. Protection of data may be required for

• legal reasons
• ethical reasons
• personal privacy
• proprietary considerations

SIAMCAT is a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. SIAMCAT is based on LASSO models, which offer distinctive advantages for model interpretation and microbial biomarker selection and avoid overfitting issues that can arise in naive combinations of feature selection and cross-validation. Part of the Microbiome Analysis Toolbox. 

The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies.  (https://pubmed.ncbi.nlm.nih.gov/32379317/)

SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is extracted from public documents and package inserts. SIDER makes available side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. It currently covers associations between 5,868 side effects and 1,430 drugs. Part of the Human Omics Analysis Toolbox. 

SIENA has been developed for the automated assembly and preprocessing of protein binding site ensembles.

The SIGnaling Network Open Resource annotates signaling information from the literature as binary causative relationships.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

Data Analysis service for ribosomal RNA

Web application to compare multiple protein structural motifs.

slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing identification of biological drivers of cell-to-cell variability and model confounding factors.