Links
We present here a top list of tools/webservers.
A more exhaustive list of bioinformatics links can be accessed from this link.
DESIGN
ILLUMINA QC
MultiQC |
Aggregate results from bioinformatics analyses across many samples into a single report
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Illumina SAV |
The Sequencing Analysis Viewer (SAV) is an application that allows you, in real time, to view important quality metrics generated by the real-time analysis (RTA) software on the Illumina sequencing systems. The Sequencing Analysis Viewer can be installed on a personal workstation to view quality metrics from a remote location.
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RNA-SEQ ANALYSIS
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Degust |
RNA-seq exploration, analysis and visualisation
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ANNOTATION DATABASES
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Ensembl |
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
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GenCode |
The GENCODE Project: Encyclopædia of genes and gene variants (Human and Mouse)
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MGI |
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
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Human Protein Atlas |
The human protein atlas displays expression and localization of proteins in a large variety of normal human tissues and cancer cells.
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Lncipedia |
A comprehensive compendium of human long non-coding RNAs
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FUNCTIONAL ENRICHMENT DATABASES
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AmiGO 2 |
AmiGO is the official tool for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms.
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Babelomics |
Babelomics is a complete suite of web tools for functional analysis of genome-scale experiments.Babelomics includes tools for functional annotation of pre-selected sets of genes, such as FatiGO+, Tissue Mining Tool and MARMITE. It also includes the FatiScan tool and an improved GSEA module to find blocks of functionally related genes.
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Gene Ontology Consortium |
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
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KEGG |
KEGG: Kyoto Encyclopedia of Genes and Genomes
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MSigDB |
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.
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GeneSigDB |
The Gene Signature DataBase is a searchable database of fully traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed.
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PUBLIC REPOSITORIES
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ArrayExpress at the EBI |
ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED recommendations.The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository.
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GEO (NCBI) |
Gene Expression Omnibus: a gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval.
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SRA (NCBI) |
The Sequence Read Archive (SRA) stores raw sequencing data and alignment information from high-throughput sequencing platforms
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FUNCTIONAL ENRICHMENT ANALYSIS
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DAVID |
Database for Annotation, Visualization and Integrated Discovery.
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ENDEAVOUR |
A web resource for gene prioritization in multiple species
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Gene Set Enrichment Analysis |
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
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EnrichR |
a comprehensive gene set enrichment analysis webserver.
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Qlucore Omics Explorer |
(COMMERCIAL) Qlucore Omics Explorer allows you to work with gene expression data (RNA-seq data (also single cell), microarrays), Proteomics and Metabolomics data, miRNA data, DNA Methylation data, Flow Cytometry data and other multi-variate data.
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Genevestigator |
(COMMERCIAL) fully curated and globally normalized resource of gene expression for biopharmaceutical and medical research.
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IPA |
(COMMERCIAL) Ingenuity Pathway Analysis
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WGCNA |
weighted correlation network analysis
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iRegulon |
iRegulon is a Cytoscape plugin that detects the TF, the targets and the motifs from a set of genes.
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DATA VISUALIZATION
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IGV |
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
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MORPHEUS |
Versatile matrix visualization and analysis software
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SCOPE |
SCope is a fast, user-friendly visualization tool for large-scale scRNA-seq datasets.
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UCSC Single Cell Browser (Tools) |
The UCSC Cell Browser is a viewer for single cell data. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster-specific marker genes.
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LONG READ SEQUENCING TOOLS
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NGMLR |
Open-source method for long-read alignment. CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBio or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations.
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Sniffles |
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGMLR with the optional SAM attributes enabled.
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SINGLE CELL ANALYSIS
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Seurat |
R package designed for QC, analysis, and exploration of single cell RNA-seq data
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SCENIC |
R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
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E-LEARNING
RESOURCES
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Bioconductor |
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
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SEQanswers |
Forum for NGS applied Bioinformatics support
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BioStars |
Forum for Bioinformatics support
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REPRODUCIBLE RESEARCH
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Code Ocean |
Cloud-based computational reproducibility platform
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Zenodo |
Repository for research output
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PUBLICATION
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Orcid |
Create a research ID
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Publons |
track, verify and showcase your peer review and editorial contributions for academic journals
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Pandoc |
Universal document converter
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Elife |
Open journal for research in all areas of the life and biomedical sciences
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GigaScience |
Open access, open data, open peer-review journal focusing on ‘big data’ research from the life and biomedical sciences |
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