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
ELIXIR training platform
StatSoft Electronic Statistics Textbook
The R cookbook The R cookbook

 


RESOURCES

Bioconductor Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Bioinformatics.org Bioinformatics Resources
Omic tools Portal of bioinformatics resources
SEQanswers Forum for NGS applied Bioinformatics support
BioStars Forum for Bioinformatics support

 


REPRODUCIBLE RESEARCH

Open Science Framework Cloud-based management for scientific projects
Protocols.io Open access repository for scientific methods
Code Ocean Cloud-based computational reproducibility platform
Zenodo Repository for research output

 


PUBLICATION

Orcid Create a research ID
Publons track, verify and showcase your peer review and editorial contributions for academic journals
Mendeley Free reference management
Pandoc Universal document converter
Grammarly Free grammar checking
Elife Open journal for research in all areas of the life and biomedical sciences
F1000 Research Open journal for life scientists with open peer review
GigaScience Open access, open data, open peer-review journal focusing on ‘big data’ research from the life and biomedical sciences
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