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TO PUBLISH ON NUCLEOMICS WEBSITE (SHORTLIST)
CATEGORYTYPENAMELINKDESCRIPTION
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YDESIGNWEBSERVER
Illumina Library Prep Kit Selector
https://emea.illumina.com/techniques/sequencing/ngs-library-prep.html?langsel=/be/#
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YDESIGNWEBSERVERRNASeq Power calculator
http://www2.hawaii.edu/~lgarmire/RNASeqPowerCalculator.htm
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YILLUMINA QCTOOLMultiQChttps://multiqc.info/Aggregate results from bioinformatics analyses across many samples into a single report
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YILLUMINA QCTOOLIllumina SAV
http://emea.support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html?langsel=/be/
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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YILLUMINA QCTOOLIllumina bcl2fastq2
http://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html?langsel=/be/
convert BCL files to FASTQ file formats
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YILLUMINA QCWEBSERVER
Illumina NextSeq500 Specifications
https://emea.illumina.com/systems/sequencing-platforms/nextseq/specifications.html?langsel=/be/
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YILLUMINA QCWEBSERVERIllumina MiSeq Specifications
https://emea.illumina.com/systems/sequencing-platforms/miseq/specifications.html?langsel=/be/
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YILLUMINA QCWEBSERVER
Illumina HiSeq4000 Specifications
https://emea.illumina.com/systems/sequencing-platforms/hiseq-3000-4000/specifications.html
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YILLUMINA QCWEBSERVER
Illumina NovaSeq6000 Specifications
https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html
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YRNA-SEQ ANALYSISWEBSERVERDegusthttp://degust.erc.monash.edu/RNA-seq exploration, analysis and visualisation
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YRNA-SEQ ANALYSISWEBSERVER
BioCyc RNA-Seq Analysis Service
http://bioinformatics.ai.sri.com/omics/(COMMERCIAL)
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YANNOTATION DATABASESWEBSERVEREnsemblhttps://www.ensembl.org/index.htmlEnsembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
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YANNOTATION DATABASESWEBSERVERGenCodehttps://www.gencodegenes.org/The GENCODE Project: Encyclopædia of genes and gene variants (Human and Mouse)
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YANNOTATION DATABASESWEBSERVERBioMart data mining tool
https://www.ensembl.org/biomart/martview
Extracting data from Ensembl using BioMart tools
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YANNOTATION DATABASESWEBSERVERMGIhttp://www.informatics.jax.org/Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
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YANNOTATION DATABASESWEBSERVERHuman Protein Atlashttps://www.proteinatlas.org/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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YANNOTATION DATABASESWEBSERVERLncipediahttps://hg38.lncipedia.org/A comprehensive compendium of human long non-coding RNAs
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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVERAmiGO 2http://amigo.geneontology.org/amigo
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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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVERBabelomicshttp://babelomics.bioinfo.cipf.es/
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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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVERGene Ontology Consortiumhttp://www.geneontology.org/The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVERKEGGhttps://www.genome.jp/kegg/KEGG: Kyoto Encyclopedia of Genes and Genomes
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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVERMSigDB
http://software.broadinstitute.org/gsea/msigdb
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.
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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVERGeneSigDBhttps://www.genesigdb.org/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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YFUNCTIONAL ENRICHMENT DATABASESWEBSERVER
Gorilla (Gene Ontology enRIchment anaLysis and visuaLizAtion tool)
http://cbl-gorilla.cs.technion.ac.il/GOrilla is a tool for identifying and visualizing enriched GO terms in ranked lists of genes.
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YPUBLIC REPOSITORIESWEBSERVERArrayExpress at the EBIhttps://www.ebi.ac.uk/arrayexpress/
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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YPUBLIC REPOSITORIESWEBSERVERGEO (NCBI)https://www.ncbi.nlm.nih.gov/geo/
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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YPUBLIC REPOSITORIESWEBSERVERSRA (NCBI)https://www.ncbi.nlm.nih.gov/sraThe Sequence Read Archive (SRA) stores raw sequencing data and alignment information from high-throughput sequencing platforms
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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVERDAVIDhttps://david.ncifcrf.gov/home.jspDatabase for Annotation, Visualization and Integrated Discovery.
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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVERENDEAVOURhttps://endeavour.esat.kuleuven.be/A web resource for gene prioritization in multiple species
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YFUNCTIONAL ENRICHMENT ANALYSISTOOLGene Set Enrichment Analysis
http://software.broadinstitute.org/gsea/index.jsp
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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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVERWEbGestalthttp://www.webgestalt.org/WEB-based GEne SeT AnaLysis Toolkit
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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVEREnrichRhttp://amp.pharm.mssm.edu/Enrichr/a comprehensive gene set enrichment analysis webserver.
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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVERQlucore Omics Explorerhttps://www.qlucore.com
(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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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVERGenevestigatorhttps://genevestigator.com/gv/(COMMERCIAL) fully curated and globally normalized resource of gene expression for biopharmaceutical and medical research.
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YFUNCTIONAL ENRICHMENT ANALYSISWEBSERVERIPA
https://www.qiagenbioinformatics.com/
(COMMERCIAL) Ingenuity Pathway Analysis
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YFUNCTIONAL ENRICHMENT ANALYSISTOOLWGCNA
https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/
weighted correlation network analysis
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YFUNCTIONAL ENRICHMENT ANALYSISTOOLiRegulonhttp://iregulon.aertslab.org/iRegulon is a Cytoscape plugin that detects the TF, the targets and the motifs from a set of genes.
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YDATA VISUALIZATIONTOOLCytoscapehttp://cytoscape.org/Biological networks
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YDATA VISUALIZATIONTOOLIGV
http://software.broadinstitute.org/software/igv/home
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
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YDATA VISUALIZATIONWEBSERVERMORPHEUS
https://software.broadinstitute.org/morpheus/
Versatile matrix visualization and analysis software
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YDATA VISUALIZATIONWEBSERVERVenny
http://bioinfogp.cnb.csic.es/tools/venny/
Venn Diagrams
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YDATA VISUALIZATIONWEBSERVERSCOPEhttp://scope.aertslab.orgSCope is a fast, user-friendly visualization tool for large-scale scRNA-seq datasets.
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YDATA VISUALIZATIONTOOL
UCSC Single Cell Browser (Tools)
https://github.com/maximilianh/cellBrowser
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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YDATA VISUALIZATIONTOOL10X Cell Loupe
https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab
Interactive Analysis
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YLONG READ SEQUENCING TOOLSTOOLNGMLRhttps://github.com/philres/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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YLONG READ SEQUENCING TOOLSTOOLSniffles
https://github.com/fritzsedlazeck/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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YLONG READ SEQUENCING TOOLSTOOLwtdbg2https://github.com/ruanjue/wtdbg2
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YLONG READ SEQUENCING TOOLSTOOLNanoR
Tool (R package) https://github.com/davidebolo1993/NanoR
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YSINGLE CELL ANALYSISTOOL10X Cell Ranger
https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#cellrangertab
Single Cell Analysis Pipelines
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YSINGLE CELL ANALYSISTOOLSeurathttps://satijalab.org/seurat/R package designed for QC, analysis, and exploration of single cell RNA-seq data
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YSINGLE CELL ANALYSISTOOLSCENIChttps://github.com/aertslab/SCENICR package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
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YE-LEARNINGWEBSERVERTraining.galaxyproject.orgTraining.galaxyproject.orgCollection of tutorials developed and maintained by the worldwide Galaxy community
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YE-LEARNINGWEBSERVERELIXIR training platform
https://www.elixir-europe.org/platforms/training
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YE-LEARNINGWEBSERVERStatSofthttp://www.statsoft.com/TextbookElectronic Statistics Textbook
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YE-LEARNINGWEBSERVERThe R cookbookhttp://www.cookbook-r.com/The R cookbook
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YRESOURCESWEBSERVERBioconductorhttp://www.bioconductor.org/Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
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YRESOURCESWEBSERVERBioinformatics.orghttp://www.bioinformatics.org/Bioinformatics Resources
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YRESOURCESWEBSERVEROmic toolshttps://omictools.com/Portal of bioinformatics resources
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YRESOURCESWEBSERVERSEQanswers
http://seqanswers.com/forums/forumdisplay.php?f=18
Forum for NGS applied Bioinformatics support
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YRESOURCESWEBSERVERBioStarshttps://www.biostars.org/Forum for Bioinformatics support
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NDNA TESTINGWEBSERVERNebula Genomicshttps://www.nebula.org/
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NDNA TESTINGWEBSERVER23andmehttps://www.23andme.com/en-int/
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NDNA TESTINGWEBSERVERDNA testing guidehttp://dnatestingguides.comThe Ultimate Scientific Guide To DNA Testing
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NDNA TESTINGWEBSERVERDarmFlora Project
http://www.vib.be/nl/mens-en-gezondheid/darmflora-project/Pages/default.aspx
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NDNA TESTINGWEBSERVERDanteLabhttps://www.dantelabs.com/
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NDNA TESTINGWEBSERVERPrometheasehttps://promethease.com/
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YREPRODUCIBLE RESEARCHWEBSERVEROpen Science Frameworkhttps://osf.io/Cloud-based management for scientific projects
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YREPRODUCIBLE RESEARCHWEBSERVERProtocols.iohttps://www.protocols.io/Open access repository for scientific methods
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YREPRODUCIBLE RESEARCHWEBSERVERCode Oceanhttps://codeocean.comCloud-based computational reproducibility platform
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YREPRODUCIBLE RESEARCHWEBSERVERZenodohttps://zenodo.org/Repository for research output
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YPUBLICATIONWEBSERVEROrcidhttps://orcid.org/Create a research ID
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YPUBLICATIONWEBSERVERPublonshttps://publons.comtrack, verify and showcase your peer review and editorial contributions for academic journals
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YPUBLICATIONWEBSERVERMendeleyhttps://www.mendeley.comFree reference management
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YPUBLICATIONWEBSERVERPandochttps://pandoc.orgUniversal document converter
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YPUBLICATIONWEBSERVERGrammarlyhttps://www.grammarly.comFree grammar checking
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YPUBLICATIONJOURNALElifehttps://elifesciences.org/Open journal for research in all areas of the life and biomedical sciences
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YPUBLICATIONJOURNALF1000 Researchhttps://f1000research.com/Open journal for life scientists with open peer review
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YPUBLICATIONJOURNALGigaScience
https://academic.oup.com/gigascience
Open access, open data, open peer-review journal focusing on ‘big data’ research from the life and biomedical sciences
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