Services

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.

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.

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

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. 

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

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.

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches. It contains manually curated models for more than 1,200 protein domains. In its ‘Genomic’ mode, it annotates proteins from completely sequenced genomes of 2,031 species as a basis for their functional annotation. It provides flexible tools to visually explore protein domain architectures across sequences and organisms. Part of the Human Omics Analysis Toolbox. 

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module.

Structural and physico-chemical interpretation of QSAR models

SQANTI3 is the first module of the [Functional IsoTranscriptomics (FIT)](https://tappas.org/) framework, which also includes IsoAnnot and tappAS.

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2, performing the following analysis steps:

1. Index the genotype file
2. Preprocess the transcript expression data
3. Test for association between splicing ratios (a multivariate phenotype) and genetic variants in cis (nominal pass)
4. Obtain an empirical P-value for each phenotype (permutation pass, optional)
5. Control for multiple testing.

Analysis workflow for plant sRNA sequencing data.

Software for Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation.

 SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. It provides the functionality of SSAMs most popular and widely used features in a graphical user interface with a few functions added for convenience and ease of use. It can be run on a modest laptop.

StructureProfiler is a tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods.

SweeD is a high-performance computing software that detects the site of the beneficial mutation, using the Site Frequency Spectrum. It can analyze whole genome data of thousands of individuals in a few hours.