Genome Biology Genetics Biostatistics R Population Genetics Genetic Epidemiology HLA MHC Homepage
BIOINFORMATICS TOOLS
(for Genetic Epidemiologists)
Open Access Reviews / Journals
ENCODE Resources (Pazin MJ. CSHP 2015); Database Tools (Bianco, Genomics 2013; Zou, 2015); UCSC Browser (Mangan, 2014)
Journals: Nucleic Acids Research (NAR); NAR Genomics & Bioinformatics; Database; Bioinformatics
Nucleic Acids Research Databases Catalog
Article Collections
ENCODE (Web Focus) FANTOM5 (RIKEN) IHEC Epigenome RoadMap TCGA GTEx
Societies
Online Suites
Galaxy (101 - Support) ExPASy (ref) Taverna 2.5.0/Archive (ref) Apache-Taverna BioMart (ref) Artemis (manual) Babelomics (ref / tutorial)
Bioconductor (manual) BioPython (tutorial & cookbook / PDF)
EDGE: Empowering the Development of Genomics Expertise (ref)
Genome Statistics
NCBI Genome (GRCh38.p14) NCBI Human Gene List Genecode HGNC Ensembl Panther (Human)
Biomarts
Ensembl BioMart (YouTube tutorial) UCSC Table Browser GWAS Central GWAS Mart (tutorial) SPS Mart (allele freqs) Fantom5
Genome Browsers
BioTools: Genome Visualization
UCSC Human Genome BioInformatics GENCODE FANTOM5 (ref / tutorial / wiki / user guide (pp.12-19)) - ZENBU - SLIDEBASE (tutorial)
Ensembl Genome Browser (Human) PopHuman (ref)
NIH RoadMap Epigenomic Browser (tutorial) WashU EpiGenome Human Epigenome Atlas NCBI Epigenomics (help) NGSmethDB (ref)
1KG (Browser - Quick Start Guide)-(NCBI)
UK10K (ref) GENCODE Browser SNiPA (gnomAD) genome Aggregation Browser (ref)
CNV Browser DECIPHER eQTL Browser seeQTL GTEx eQTL Browser
lncRBase NonCode FANTOM CAT (lncRNA Atlas) Browser (ref) Integrative Genomics (ref)
VISTA Enhancer Browser Swiss Regulon Reactome Pathway Browser ImmunoBase Browser ImmunPop Browser (ref)
NCBI Genome Data Viewer (GDV) (ref / tutorial)
General Resources
NCBI Global Search GoPubMed HuGE LabMeeting NCBI Tutorials / Handbook / Help Manual NIH Helix NCBI Tools for Data Mining NCI Data Analysis Tools
Sanger: Software / Databases & Tools EMBL-EBI Swiss Institute of Bioinformatics: ExPASy
NCBI Gene .. GeneCards (User Guide) .. GeneMap .. GenAtlas .. iHOP .. BioGPS Gene Annotation .. Harmonizome (ref)
NCBI (tutorials on YouTube) .. BLAST .. MimicMe (ref) .. e-PCR .. In Silico PCR .. GeneNote .. GeneLoc .. CGAP-GAI .. Aceview
ENCODE (ref / tutorial1 / tutorial2 / cell types) GENCODE RegulomeDB FANTOM/Gateway (papers / software) Broad Institute Portals
Database of Genomic Variants (CNV) CNV inspector Copy Number Variation Resources DECIPHER (ref)
OMIM .. OMIM Map .. NCBI Genetic Association Database (GAD) [Now Retired] .. HuGE Navigator .. Variant Name Mapper
Gene Exp Omnibus -GEO (NCBI) .. NCBI dbGaP .. ArrayExpress (EBI) .. SOURCE (genomics tool)
Comparative Toxicogenomics Database (CTD) CHE Toxicant & Disease Database CellTypist (ref)
NIEHS SNPs RNA-seq Atlas (via OmicTools) (ref) NGSmethDB (ref) MecCog (genetic disease mechanisms) (ref / tutorial)
Genomic coordinate conversion: Ensembl Assembly Converter Kaviar
Harmonizome (ref) iLINCS (ref) SigComLINCS (ref) GeneHopper (ref)
SNP Resources (variation & functional annotation)
BioTools: SNP NAR Database: Polymorphism Dr Martti's Tools: SNP SNP Notes
VarNote-REG (ref) AnnoPortal (ref) CAUSALdb (ref / documentation) SNP-SuRE (ref) FeatSNP 3DSNP v2.0 (ref / tutorial)
OpenTargets (ref1 / ref2) OpenTargets PostGWAS- GitHub Mastermind (ref) varsome (ref) monarch (ref)
VariED (ref) LDtrait (ref) UCSC Variant Annotation Integrator (VAI) VARAdb (ref)
dbSNP (help / tutorials / variation services) LOVD (ref) NCI LDLink (ref) PER (Pathogenic variant-enriched regions) (ref)
NCBI Variation Viewer NCBI ClinVar (ref) NHGRI Clin Genomic DB GeneSNPs PharmGKB HGMD snpXplorer (ref / GitHub)
Ensembl Variant Effect Predictor (VEP) AVIA (ref / tutorial) wANNOVAR (tutorial) FunSeq2 (ref) dbNSFP (ref) Variant Ranker (ref / tutorial)
rVarBase (ref / tutorial) SNiPA (ref) DICE (Dbase of Immune Cell Eqtl/Exp/Epigen) (ref)
mQTLdb (ref) GoDMC (ref) DiseaseMeth (ref)
SNPnexus (User Guide) .. PheGenI (tutorial) .. HaploReg v4 (ref) .. HumanMine (ref) .. CoreMine .. VaDE .. SNVrap/QUICKrap (ref)
FUN-LDA (ref) CADD (ref1 / ref2) .. DANN (ref) .. EIGEN (ref) .. FATHMM (ref) .. GWAVA (ref) .. SusPect (ref) .. RegulomeDB (GWAS) .. DeepSEA (ref)
FATHMM-XF (ref) PhD-SNPg (ref) PredictSNP2 (ref) SNPDelScore (ref) PAFA (ref) FINSURF (ref) UMD-Predictor (ref)
RVS / Reference Variant Store (ref) Structure PPi (ref) GenoCanyon (ref) ClinGen Pathogenicity Calculator (ref)
VarioWatch .. SNPedia .. NextBio .. SNPwatch .. MutaGeneSys .. LS-SNP/PDB .. LS-SNP (ref)
dSysMap (ref / tutorial) PsyGeNET (ref1/ref2)
rSNP Guide .. SNPLogic .. SPSMart (comparative frequencies)
DistiLD .. SNPEffect .. SNPfunc (ref) .. GRAIL (ref)
PopHuman (ref) Haplotter HGDP Selection Browser Selectome - A Database of Positive Selection dbPSHP (ref) GERP (ref1 / ref2)
FERRET for 1KG SNP Data Download (ref) – requires JAVA SNP2Gene (physical mapping)
Obsolete: GENEPI TOOLBOX (ref) OpenTargets PostGWAS (ref) BIOS QTL Browser (ref1 / ref2)
Proxy Search
NCI LDLink (ref) NCI_LDproxy (ref) NCI LDAssoc (ref) NCI LDexpress (ref) NCI SNPclip (pruning) (ref)
ssSNPer .. SNAP .. SNPSnap (ref / guide) .. SPOT (ref / user guide) .. HaploReg v4 .. CandiSNPer (ref)
Obsolete: rAggr
eQTL / meQTL Resources
BioTools: eQTL BioTools: meQTL
EMBL-EBI eQTL Catalog (ref / training webinar) FIVEx (ref / GitHub) eQTLGen (ref) QTLizer (ref)
GTEx .. NCBI Molecular QTL Browser (ref) .. SCAN (tutorial) .. PheGenI .. eQTL Databases
ESM_Browser (Exonic Splicing Mutations) (ref)
eQTL Resources @ Pritchard Lab (browser) .. eQTL Catalog (NESDA/NTR) (ref) .. reQTL (ref)
CAGE eQTL Browser (ref) ImmunPop eQTL Browser (ref) GEUVADIS/1KG (ref; data download)
mQTLdb (ref) GoDMC (ref) LIBD (Brain) eQTL Browser (ref)
HSM (Haplotype-specific Methylation-associated SNPs) (ref) EpiDelta (ref) DiseaseMeth (ref)
Plateletomics (platelet transcriptomics by gender) ImmGen eQTL Browser (mouse)
FIRE (Functional Inference of genetic variants that Regulate gene Expression) (ref)
eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual) PancanQTL (ref) Pancan meQTL (ref)
Obsolete: seeQTL (ref) .. e/meQTL .. GWAS2Genes (ref) .. Blood eQTL Browser .. BIOS QTL Browser (ref1 / ref2)
Splice Site Analysis and ssSNPs / RNA Modifications
FIVEx (ref / GitHub) regSNPs-splicing (ref) dbNSFP (ref) ESM_Browser (Exonic Splicing Mutations) (ref)
AS-ALPS (ref) NNSplice (splice site prediction on genomic sequence) Human Splicing Finder Splice-Net DBSCSNV (splice site SNPs) (ref)
Splice Disruption Model SNPs @ GTEx BPHunter (Branch Point SNPs) (ref) ValidSpliceMut (ref) RMvar (RNA modificating SNPs) (ref) RMDisease (ref / user guide)
Obsolete: ssSNPTarget (ref) .. AASsites (ref)
Coding SNP Annotation
genome Aggregation (gnomAD) Browser (formerly ExAc Browser) (ref)
MISCAST (ref) Variant Score Ranker (ref) Rhapsody (ref)
Missense3D-DB (ref) .. SNPs3D .. dbNSFP (ref) .. SNPdbe (ref) .. PolyPhen-2 .. SIFT (by SNP ID) .. PolyDoms .. KD4v (ref)
MutDB .. HGMD .. Panther (download) .. FannsDB (Condel & TransFIC) .. Mutation Assessor (ref) .. MutPred .. PMut (ref)
GWAS Resources
BioTools: GWAS Dr Martti's: GWAS Tools
OpenTargets (ref1 / ref2) Mastermind (ref) VariED (ref) LDtrait (ref) PhenoScanner (manual / ref) TreeWAS (ref / FAQs)
CTG postGWAS: Browser & Virtual Lab (ref) XGR for Genes/SNPs (ref / R package / demo)
EBI GWAS Catalog (ref) NCBI GAPplus GWAS Explorer (ref) GWAS Central HuGE Navigator
TCGD Cancer GWAS Database (ref) Cancer PRSweb (ref) PHGKB-Cancer
GRASP (ref / overview / user guide) GWAS4D (ref / help) FUMA GWAS (ref) MAGMA (ref) DEPICT (ref)
LocusZoom (ref) FORGE (ref / GitHub / Wiki) VAMPIRE (ref) pgwas (Proteo-Genomic Convergence) (ref)
GWAS-ROCS (ref) PGS Catalog v1 (ref) – v2: PRS (ref) ExPRSweb (ref) MendelVar (ref/tutorial)
HaploReg v4 (ref) RegulomeDB (GWAS) OpenTargets – V2D
GenAMap (ref / tutorial) SNPTrack (ref)
OMICtools GWAS Diagram Browser SIB Association Viewer (ref)
SNP Imputability HLA-IMP (tutorial/ref)
CAPE: CellulAr dePendent dEactivating mutations predictor (ref)
GARLIC: GWAS-based Prediction Toolkit for Connecting Diseases and Cell Types (ref)
LD Hub (ref) easyGWAS (ref / tutorial) UKBB Heritability Browser GWEHS (ref/Wiki)
LDGIdb (Linkage-Disequilibrium-based Gene Interaction database) (ref)
CGEMS (KM Plotter) Human Protein Atlas KM Plotter - Search (ref) Adult Human Cell Atlas (AHCA) (ref)
GeneAtlas (UK Biobank) GeneAtlas/PheWAS PheWeb (UK Biobank) (unpublished) PheWAS Catalog UKBB-GeneBass (ref)
FinnGene GWAS Browser (ref) MGeND (Medical Genomics Japan Variant Database) (ref)
Metabolomics GWAS mGWAS (ref) PGWAS: Proteomics GWAS (ref) pgwas (ref) Omicscience (ref)
eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual)
humanbase (module/GWAS)
GWAS Summary Results: EBI GWAS Catalog GRASP GWAS-ATLAS (Atlas of GWAS Summary Statistics) (ref)
Obsolete: MR-Base (ref1 / ref2) HESS: Heritability Estimation from Summary Statistics of GWAS (ref) WGAviewer (ref) GWATCH (ref) GWASKB (ref / GitHub)
GWASdb v2 (ref) Breast Cancer GWAS: GAME-ON
Epigenetics
BioTools: Epigenetics EpiGenie Epigenetics Tools EpiMap / Browser (ref) EpiDelta (ref) ImmuMethy (ref)
NIH RoadMap Epigenomic Browser (tutorial / cell types) WashU EpiGenome Human Epigenome Atlas NCBI Epigenomics (help)
Int Hum Epigenet Cons (IHEC) IHEC Data Portal FeatSNP
HEDD (Human Epigenetic Drug Database) (ref)
EWAS Catalog (ref) EWAS Atlas (ref) eFORGE (ref) EWAS Cat (Summary Stats) Table of All EWAS
CpG Sites List (CruzDB) SNPs to CpG Islands (ref)
Obsolete: EpiRegNet (ref)
Chromatin Features Databases
HEDD (Human Enhancer Disease Database) (ref) DiseaseEnhancer (Disease-associated enhancers) (ref) GeneHancer (ref)
SlideBase (FANTOM Enhancers) (tutorial) epiTAD (ref) ABC Enhancer-Gene Connections (ref) EnhancerDB (ref)
EpiRegio (ref / documentation) EpiFactors (ref) HeRA (ref) CATlas (ref)
descartes (Cell Atlas of Fetal Development) (ref1 / ref2)
Cistrome DB (for chromatin features) (ref) NHGRI HistoneDB v.2 (ref)
3DIV (3D-genome Interaction Viewer and Database) (ref1 – ref2 / tutorial)
3D Genome Browsers: Yue Lab (ref / tutorial) HUGIn (ref / tutorial) 3DGB/McGill (ref) 3Disease Browser (ref / tutorial)
4D Genome (ref) 3CDB (ref) Human Histone Modification Database (HHMD) (ref)
Obsolete: CCSI (ref)
ncRNA (microRNA/lncRNA) & Pseudogene Resources
BioTools: microRNA BioTools: lncRNA / BioTools: lincRNA BioTools: ncRNA
NONCODE (ref) NONCODER (ref) NPInter v3 (ref) ncRNA Databases Resource (NRDR) ChIPBase (ref)
miRBase miRDB mrSNP TargetScan (ref) miRWalk 2.0 (ref) StarBase (tutorial / ref) miRNA SNiPer (ref) microSNiPer (ref)
DIANA-TarBase (ref) miRTarBase (ref-2014 / 2016) miRmap (ref) miRNAmap (tutorial/ref) Human miRNA Tissue Atlas (ref) miRFocus
Human miRNA Disease Database (HMDD) ncFANs (ref)
miRCancer miR-TV (ref) OncomiR (ref) OncomiRDB (ref) leukmir (ref) mirAPP (ref) HOCTAR (ref) FAME (ref) IntaRNA (ref / help)
RegNetwork (TF and miRNA networks) (ref) Genome-wide Predictions of miRNA Regulation by Transcription Factors Database (ref)
miRNA-SNP db (ref) AVIA miR SNP Analysis Tool miTranscriptome (ref) iSeeRNA (ref) miRcode (ref)
FANTOM CAT/lncRNA Atlas / Browser (ref) MNDR (Mammal ncRNA-Disease Repository) (ref)
lncRNA and Disease Database lncTar for Target Prediction (ref) lncRNAMap (ref) LncMAP (ref)
LNCiPedia (ref) lnCeDB (ref) lncRBase (ref) DIANA-lncBase (ref / v2.0) LncRNADisease v2 (ref1 / ref2)
EVLncRNAs (database for long non-coding RNAs) (ref) ncRNA (Functional RNA Analysis)
Lnc2Meth (database of regulatory relationships between long non-coding RNAs and DNA methylation) (ref)
lnCaNet Database (lncRNA-Cancer co-expression database) (ref) lncRNA-SNP db (ref) LncVar (ref)
lncScape (Hematopoietic lineage and leukemia lncRNA expression atlas) (ref) ImmLnc (immune lncRNAs in cancer) (ref)
IntaRNA (ncRNA-mRNA interaction prediction) (ref)
Database of small human noncoding RNAs (DASHR) (ref) miRVaS (miRNA search within sequences) (ref / manual)
PseudoMap (ref / tutorial) RNASNP (Predicting SNP effects on local RNA secondary structure) RBP-Var2 (ref)
Obsolete: lncRNome (ref) lncRNA2Target (ref) lncRNA2Function (ref) lncReg (ref) lncRNAtor (ref) Co-LncRNA (ref) TF2LncRNA (ref)
LincSNP v2 (ref) decodeRNA (ref)
Gene Expression (incl. cancer) & Cancer Informatics
Cancer Cell Line Encyclopedia / CCLE (ref) Human Protein Atlas: Cancer RefEx (ref) descartes (Cell Atlas of Fetal Development) (ref1 / ref2)
RNA-seq Atlas (ref) Expression Atlas (ref) lnCaNet Database (ref) PanglaoDB (ref)
TSEA (Tissue Specific Expression Analysis) (ref) SC2disease (ref)
PancanQTL (ref) Pancan meQTL (ref)
NCI Genomic Data Commons (GDC) (ref)
Cancer Gene Census (ref) Network of Cancer Genes (ref) CHG: Cancer Hallmark Genes (ref / download)
PeCan (St Jude Pediatric Cancer Genetics) (ref / tutorial)
ORGANize (linking genes to the organs they affect) (ref / help)
SAGD (sex-associated gene database from transcriptomes) (ref)
Gene Enrichment Profiler (ref) DiRE (Distant Regulatory Elements of Co-regulated Genes) (ref)
Brain: Oxford Brain Imaging Genetics (BIG) Server v2 OASIS Brain (ref) Cortecon (ref) BrainSpan (ref / help) CrispBrain (ref)
FeatSNP (Brain-Specific Epigenetic Annotation of Human SNPs) (ref) meQTLs in Human Brain (ref) BrainSeq (eQTL) (ref)
&
(KM Plotter) Human Protein Atlas KM Plotter (ref) TCGA Survival (ref)
Databases for Cancer Genomics (Table 2 in Chin, 2011)
Transcription Factor Binding Site Search
GVATdb (Genetic Variants Allelic TF Binding Database) (ref)
ADASTRA (Allele-Specific Transcription Factor Binding Sites) (ref) - includes Androgen Receptor
Harmonizome: ENCODE Transcription Factor Binding Sites (enter the TF in Filter box)
Harminozome: MotifMap Predicted Transcription Factor Targets (enter the gene in Filter box)
TransFac TFBS Search (Qiagen) TFBS Mapper (ref) TFBIND MFold JasPar (ref) PAZAR SNP@llincRNA TFBS (ref) @SNP (ref)
Swiss Regulon AR Target Gene Dbase TESS-discontinued
Cancer Somatic Mutations
COSMIC (somatic mutations in cancer) .. COSMIC Browser .. ICGC Data Portal .. NCBI Cancer Genome Anatomy Project .. cBioPortal
HotSpotAnnotations (ref) CancerVar (ref / GitHub)
Integrative OncoGenomics Database (intOgen) (ref) DriverDBv2 (ref, help) OncodriveFML (ref)
CRAVAT (ref / help) CIViC (ref) TCGA Clinical Explorer
TransFIC PRISMAD (ref) BRCA1 Circos (ref) Cancer cell line encyclopedia (CCLE) (ref)
(See also Yang, 2015 & Raphael, 2015)
Gene Set Enrichment and Pathway Analysis
ENRICHR (ref / help) SigComLINCS (ref) GSEA/MSigDB (User Guide) GSAn [GO only] (ref / user guide) ConsensusPath (CPdB) (ref / protocol / documentation)
Pathway Commons (guide / primer / tutorial1 & 2) Pathview (ref)
DAVID (ref / tutorial / protocol) SSEA (ref) g:Profiler (ref / protocol) Varanto (SNP to Pathway) (ref) TissueEnrich (ref) XGR for Genes/SNPs (ref / R package / demo)
KEA3 (Kinase Enrichment Analysis) (ref) X2Kweb (Expression to Kinases) (ref)
Cytoscape Disease Connect ToppGene (ref) Panda (ref / video tutorial) WebGestalt (ref) IMPaLA (ref) Metascape (ref)
UniHi Reactome (user guide) Reactome Pathway Browser BioSystems Pathway Searcher KEGG KeggExp (for visualisation) (ref)
Gene Ontology GeneSetDB GeneFamilies
PCxN - The Pathway Co-Activity Map (ref) SIGNAL (ref / User Guide) HiPathia (ref / User Guide)
GSEA & GSEA-SNP GIANT (Gene Networks in Tissues; Ref) Onto-Tools (user guide)
FUMA-GENE2FUNC iLINCS (ref) RMDisease (ref / user guide) MGenrichment (microglia) (ref)
Comparative Toxicogenomics Database (CTD)
Obsolete: IPAD (ref) GeneSigDB
GWAS SNP Set Analysis
i-Gsea4Gwas Web Server (ref / tutorial) GSEA & GSEA-SNP SSEA (ref) VSEAMS (ref)-for local use MAGENTA (ref)-requires MatLab
VSEA: Variant Set Enrichment Analysis (ref)
FUMA > SNP2GENE: Functional Mapping and Annotation (ref)
Reactome via SNPnexus v4 (nearest gene algorithm)
GWAS Network Analysis
GWAB (Network-based Boosting of GWAS) (ref) NetWAS (ref) (example)
Gene Network Analysis
Genetic Network Analysis Tool (GNAT) (ref) Gene Network v2.0 (ref / GitHub)
GeneNetwork-UT / GN2 (co-expression) (ref) Human Gene Correlation Analysis (co-expression) (ref) CORD (ref) (co-regulation)
GLITTER (tissue-specific coexpression) (ref) iLINCS (ref) X2Kweb (Expression to Kinases) (ref)
GIANT (Gene Networks in Tissues; ref) BioGrid String
RegNetwork (TF and miRNA networks) (ref) ChIPBase (ref)
Genome-wide Predictions of miRNA Regulation by Transcription Factors Database (ref)
Gene Ontology
QuickGO (ontology) .. Gene Ontology (AmiGO browser)
GeneNetwork-UCMG (function, expression and co-expression) .. GeneNetwork-UT
Immunoinformatics
IPD-IMGT/HLA (ref) MHCcluster (ref) Immune Epitope Database (IEDB) (video tutorials/ref)
HLA Epitopes @ Allele Frequencies.Net (ref) PGG.MHC (ref) HLA-EPI (Epitope Registry) (ref)
IMGT/HLA Allele Query EASY-HLA (ref) HLA3D (ref) HLA-SPREAD (ref)
ImmPort (tutorial) ImmVar ImmunoBase (browser) ImmuNet (ref) ImmuneCellScience (ref) ImmGene-Mouse (ref / video)
Cross-tissue Immune Cell Atlas (ref) ImmuMethy (ref) PCIG (PanCancerImmunoGenomics) (ref)
FineMapping / PICS (ref) SNP2HLA (Imputation of Amino Acid Polymorphisms in HLA) (ref / manual) HLA-IMPUTER (ref)
HLA-NET GENE[RATE] Tools (publications) HLA-NET: Charts & Maps
HLA-TAPAS (HLA-Typing At Protein coding positions for Association Studies) (ref)
BIGDAWG Case-Control HLA Data Analysis (ref)
MHC Haplotype Project_Archived dbMHC_Archived IDAWG_Archived Vega Genome Browser_Archived
Obsolete: The SysteMHC Atlas Project (ref)
Proteins
Human Protein Atlas (ref) .. ProteomicsDB .. Protein Data Bank .. MOPED .. SWISS-MODEL .. SwissVar .. AS-ALPS (ref)
Structure PPi (ref) Phyre 2 (ref; tutorial; tutorial notes) Phyre 2 Investigator ConsensusPath (CPdB) (ref)
SusPect (ref) UniProt (query) SwissProt Protein-Protein Interaction Mining Tool MINT (interactions)
BioPlex (ref) Genome3D SMART STRING Jet2Viewer (PPI) (ref)
Structural Biology Knowledgebase (SBKB) MEME Suite iHOP
Protein Sequence Analysis Protein Functional Analysis (PFA) @ EMBL SOSUI (ref)
ExPasy: Proteomics Tools Tools for Protein Analysis GenomeNet Chemical Analysis Tools 3DBIONETS-WS (ref)
Post-translational Modifications
PTMD (ref) MusiteDeep (ref)
GPS PhosSNP (ref) Functional Glycomics ActiveDriverDB (variation in post-translational modification sites) (ref)
Protein-related Bioinformatics Resources
Human Metabolome Database (HMDB) Metabolomics GWAS HumanMine (ref)
ANNOVAR (ref / quick startup guide / protocol) wANNOVAR (tutorial) AVIA
AURA: Atlas of UTR Regulatory Activity (ref)
PAFA: Prioritization And Functional Assessment of Variants (ref)
Disease Databases
dSysMap (ref / tutorial) Disease Connect CoreMine Phenolyzer (ref / tutorial) PhenoPred SNPs3D DisGeNET (ref) CPR Diseases (ref)
FANTOM CAT Traits Database 3Disease Browser (ref / tutorial) eDGAR (Disease-Gene Associations) (ref / tutorial) MecCog (genetic disease mechanisms) (ref / tutorial)
Comparative Toxicogenomics Database (CTD)
EpiGraphDB (ref) DiseaseMeth (ref) Geneshot (ref) SC2disease (ref)
SZGR (ref) SZDB Database (ref)
Brain xQTL Serve (ref) WGBS Brain meQTLs (ref) FeatSNP (Brain-Specific Epigenetic Annotation of Human SNPs) (ref) MGenrichment (microglia) (ref)
Alzheimer Disease Gene Exp Browser (ref) Alzheimer Disease Meta-Analysis (ref) Alzheimer Multi-Omics Landscape (ref) AlzGene (ref)
ADVP (Alzheimer Disease Variants Portal) (ref) NIAGADS (ref) AD Knowledge Portal (ref) CrispBrain (ref)
Various Other Resources
Gene Prediction Tools
AUGUSTUS Gene Prediction Tool (tutorial) Gene Prediction
TaqMan SNP Genotyping Assays (1) (2)
Chang Bioscience Tools VISTA Tools
ThermoFisher Learning Center .. Access Biotech
Restriction Enzyme Database .. NEBCutter .. GenScript Tools
Primer Design Software Primer3 (help) .. Primer3Plus .. Oligo Analyser and PrimerQuest (IDT)
FastPCR .. FastPCR Online Tools .. In Silico PCR
Multiple Sequence Alignment: Clustal (help) .. Topali v2 .. Jabaws
Expasy Translate Tool .. ORF Finder (NCBI) .. JustBio Bioinformatics Tools
Icahn School of Medicine Ma'ayan Lab Yue Lab Cui Lab Mulin Lab
Search Templates
(use these static URLs for quick searches by changing the indicated identifier to yours in the address line)
dbSNP (GeneID) dbSNP (rs#) Ensembl (rs#) SNiPA (rs#) FeatSNP (rs#)
GWAS Cat (EBI) (rs#) EWAS Cat (CpG) PhenoScanner (rs#) GeneAtlas-PheWAS (UK Biobank) (rs#) OpenGWAS (rs#)
PheGenI (rs#) dbGAP (rs#) GWAS Central (rs#) Super-EnhancerDB (rs#) GTEx (rs#) TreeWAS (rs#)
Variation Viewer (geneName) rVarBase (rs#) HaploReg v4 (rs#) HSM (rs#) 3DSNP (rs#)
SNPedia (rs#) OpenSNP (rs#) SNPDelScore (rs#): Restful (API) ClinVar (rs#)
LDAssoc / LDPair (LD between two SNPs in EUR populations)
RegulomeDB (chr#/nt#)
Ensembl (Gene Name) Gene (Gene Name1/Human) Gene (Gene Name2) Gene (GeneID)
GTeX (Gene Name) GTEx Visualizer (Gene Name) GTEx (your own SNP) GTEX (alt. splicing variants for a gene)
GWAS Central (Gene Name) Ingenuity Target Explorer (Gene Name) Harmonizome (Gene Name) Genehopper (Gene Name)
ENCODE Regulatory Elements DB (Gene Name) GenCode - Alternative Splicing Variants (Gene Name)
Expression Atlas (Gene Name) Protein Atlas (Gene Name)
COSMIC Gene Analysis Search (Gene Name)
LnCaNet search: general info by Gene ID; expression by Gene ID; PTM by Gene ID
HGMD (Gene Name) GeneCards Entrez Structure RVIS (GeneName) iLINCS Harmonizome
Amino Acids Genetic Code Ambiguity (Mixed Base) Codes
ONLINE TUTORIALS / TRAINING
BioStar Handbook: Recipes Cookbook
Babraham Bioinformatics Training Courses
EMBER - A Practical Guide to Bioinformatics
GOBLET - the Global Organisation for Bioinformatics Learning, Education & Training
Bioinformatics Labs in Virtual Labs (ref) CourseSource: Bioinformatics / Genetics
Applied Bioinformatics Course (ABC) (ref)
Bioinformatics Training and Services (BITS) - Exercises
Dr Martti's Bioinformatics Pages
Tutorials: NCBI Mini-Courses (NCBI) dbSNP Bioconductor Ensembl UCSC Haploview Galaxy GoldenHelix ImmPort
EMBL-EBI Training Getting Genetics Done BioStars
Online Lectures on Bioinformatics
Genome Biology (for Genetic Epidemiologists) & Applied Bioinformatics Course Notes
Melbourne Bioinformatics (formerly VLSCI) Genomics Virtual Laboratory (GVL) (tutorial)
Bioinformatics Labs in Virtual Labs (ref) Bioinformatics on CourseSource labXchange
Complex-Traits Genetics Virtual Lab (ref)
Center for Statistical Genetics (Uni of Michigan)
HGNC Human Genetic Nomenclature Guide
General Allele Frequency Database ALFRED HLA Allele Frequencies
R LIBRARIES to Learn/Teach R
learnr discovr (GitHub) SWIRL (courses; help) OpenIntroStat (openintro / GitHub / R Labs)
learnPopGenet (ref) refine.bio Examples
Teaching Statistics with R (CRAN Task View)
R Community Public Library of eBooks
R LIBRARIES for Bioinformatics
BioConductor Framework (packages / vignettes / workflows / help; support / tutorials / newsletter / conferences)
rentrez (vignette) haploR (vignette; ref) enrichR (ref / usage) biomaRt (user guide / vignette / examples)
gwasrapidd (ref / Getting Started / Functions / Case Study / Cheat Sheet) gwascat (vignette1 / vignette2) GWASTools (ref) GenABEL (ref)
XGR for Genes/SNPs (ref / R package / manual / demo) QTLizer (ref / GitHub) rGREAT (ref)
echolocatoR (RDRR / ref / vignette 1 / vignette 2 / GitHub) catalogueR (RDRR / ref / manual) postgwas (ref / vignette)
R-Bloggers tag: GWAS hierGWAS (tutorial) VarExp (ref / GitHub)
Bayesian GWAS Analysis: GWAS.BAYES (vignette) bGWAS (ref / GitHub) genphen (overview)
snpGeneSets (manual; ref) VSE: Variant Set Enrichment (ref / vignette1 & 2 / practical / GitHub)
traseR (ref) garfield (ref) VarGen (ref) biomartr (ref) LDlinkR (ref)
AnnotationHub (vignette1 & 2; using AH) annotatr (vignette) AnnotationDbi (vignette) rtracklayer (data import) motifbreakR (ref / manual / vignette)
GenomicFeatures (vignette) GenomicRanges (vignette1 & 2) HelloRanges (tutorial)
loci2path (ref / GitHub) deTS (ref / GitHub)
GSOAP (visualization of gene set over-representation analysis) (ref)
gprofiler2 (ref / vignette) DOSE (ref / vignette) clusterProfiler/GSEA (ref) ReactomePA enrichplot (ref / manual / vignette)
disgenet2r (ref / GitHub) CONQUER (ref)
BioMedR (ref / vignette / GitHub) HPAanalyze (ref / GitHub) GEOquery (ref / GitHub)
BIGDAWG Case-Control HLA Data Analysis (ref)
Obsolete: NCBI2R (GitHub) SuRFR (ref)
qPCR Analysis Using R
qRAT (ref) qPCRtools (GitHub / vignette) EasyqpcR (vignette) tidyqpcr (GitHub) pcr (ref / GitHub / vignette) qPCR ReadqPCR (vignette) / NormqPCR (vignette) (ref)
LINKS
Links to Bioinformatics Tools @ ABC
Bioinformatics.ca Dr Martti's Bioinformatics Pages
OMICSTools Dataset2Tools (Tools) (ref) BioTools
Online Bioinformatics Resources Collection
Genome Biology Genetics Biostatistics R Population Genetics Genetic Epidemiology HLA MHC Homepage
17 September 2023