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 Library Prep Kit Selector

RNASeq Power calculator

ILLUMINA QC

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report

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.

Illumina bcl2fastq2

convert BCL files to FASTQ file formats

RNA-SEQ ANALYSIS

Degust

RNA-seq exploration, analysis and visualisation

BioCyc RNA-Seq Analysis Service

(COMMERCIAL)

ANNOTATION DATABASES

Ensembl

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.

GenCode

The GENCODE Project: Encyclopædia of genes and gene variants (Human and Mouse)

BioMart data mining tool

Extracting data from Ensembl using BioMart tools

MGI	Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.

Human Protein Atlas

The human protein atlas displays expression and localization of proteins in a large variety of normal human tissues and cancer cells.

Lncipedia

A comprehensive compendium of human long non-coding RNAs

FUNCTIONAL ENRICHMENT DATABASES

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.

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.

Gene Ontology Consortium

The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

KEGG	KEGG: Kyoto Encyclopedia of Genes and Genomes

MSigDB

The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.

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.

Gorilla (Gene Ontology enRIchment anaLysis and visuaLizAtion tool)

GOrilla is a tool for identifying and visualizing enriched GO terms in ranked lists of genes.

PUBLIC REPOSITORIES

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.

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.

SRA (NCBI)

The Sequence Read Archive (SRA) stores raw sequencing data and alignment information from high-throughput sequencing platforms

FUNCTIONAL ENRICHMENT ANALYSIS

DAVID

Database for Annotation, Visualization and Integrated Discovery.

ENDEAVOUR

A web resource for gene prioritization in multiple species

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).

WEbGestalt

WEB-based GEne SeT AnaLysis Toolkit

EnrichR

a comprehensive gene set enrichment analysis webserver.

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.

Genevestigator

(COMMERCIAL) fully curated and globally normalized resource of gene expression for biopharmaceutical and medical research.

IPA	(COMMERCIAL) Ingenuity Pathway Analysis

WGCNA

weighted correlation network analysis

iRegulon

iRegulon is a Cytoscape plugin that detects the TF, the targets and the motifs from a set of genes.

DATA VISUALIZATION

Cytoscape

Biological networks

IGV	The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

MORPHEUS

Versatile matrix visualization and analysis software

Venny

Venn Diagrams

SCOPE

SCope is a fast, user-friendly visualization tool for large-scale scRNA-seq datasets.

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.

10X Cell Loupe

Interactive Analysis

LONG READ SEQUENCING TOOLS

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.

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.

wtdbg2

NanoR

SINGLE CELL ANALYSIS

10X Cell Ranger

Single Cell Analysis Pipelines

Seurat

R package designed for QC, analysis, and exploration of single cell RNA-seq data

SCENIC

R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

E-LEARNING

Training.galaxyproject.org

Collection of tutorials developed and maintained by the worldwide Galaxy community