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BIOINFORMATICS TOOLS

(for Genetic Epidemiologists)

Mehmet Tevfik DORAK, MD, PhD

 

Open Access Reviews / Journals

ENCODE Resources (Pazin MJ. CSHP 2015); Database Tools (Bianco, Genomics 2013; Zou, 2015); UCSC Browser (Mangan, 2014)

JournalsNucleic Acids Research (NAR); NAR Genomics & Bioinformatics;  Database; Bioinformatics  

 Nucleic Acids Research Databases Catalog

Scientific Data

 

Article Collections

 ENCODE (Web Focus)     FANTOM5 (RIKEN)    IHEC    Epigenome RoadMap     TCGA     GTEx

F1000Research: Bioconductor

 

Societies

ISCB     ISMB    AMIA   ECCB

 

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)

 

Biomarts

BioTools: Biomart

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)   Vega Genome Browser (Human)

NIH RoadMap Epigenomic Browser (tutorial)   WashU EpiGenome   Human Epigenome Atlas   NCBI Epigenomics (help)   NGSmethDB (ref)

1KG (Browser - Quick Start Guide)-(NCBI)   PopHuman (ref)

  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)

 

 General Resources

BioTools    OmicX

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   JJ Wang Lab

NCBI Gene .. GeneCards .. 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  

  NIEHS SNPs    RNA-seq Atlas (via OmicTools) (ref)   NGSmethDB (ref)

Genomic coordinate conversion: Ensembl Assembly Converter   Kaviar

rsID to VCF conversion: dbSNP  

Harmonizome (ref)

 

 SNP Resources (variation & functional annotation)

BioTools: SNP      NAR Database: Polymorphism    Dr Martti's Tools: SNP

OpenTargets    OpenTargets PostGWAS   Mastermind (ref)   VariED (ref)   LDtrait (ref)   UCSC Variant Annotation Integrator (VAI)

dbSNP .. dbSNP Tutorial   LOVD (ref)   NCI LDLink (ref

NCBI Variation Viewer   NCBI ClinVar (ref)  NHGRI Clin Genomic DB   GeneSNPs   PharmGKB   HGMD

Ensembl Variant Effect Predictor (VEP)     AVIA  (ref / tutorial)     wANNOVAR (tutorial)    FunSeq2 (ref)

rVarBase (ref / tutorial)   SNiPA (ref)   mQTLdb (ref)   BIOS QTL Browser (ref1 / ref2)   DICE (Dbase of Immune Cell Eqtl/Exp/Epigen) (ref)

SNPnexus (guide) .. PheGenI (tutorial) .. HaploReg v4 (ref) .. HumanMine (ref) .. CoreMine .. VaDE .. SNVrap/QUICKrap (ref)  

FUN-LDA (ref)   CADD (ref) .. DANN (ref) .. EIGEN (ref) .. FATHMM (ref) .. GWAVA (ref) .. SusPect (ref) .. RegulomeDB (GWAS) .. DeepSEA (ref)

FATHMM-XF (ref)  PhD-SNPg (refPredictSNP2 (refSNPDelScore (ref)  PAFA (ref)  ClinGen Pathogenicity Calculator (ref)   UMD-Predictor (ref)

 RVS / Reference Variant Store (ref)     Structure PPi (ref)     GenoCanyon (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)

RVIS Genic Intolerance (ref)

 FERRET for 1KG SNP Data Download (ref)

GENEPI TOOLBOX (ref)   Endeavour

Harmonizome (ref)

 

Proxy Search

NCI LDLink (refNCI LDAssoc (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)

GTEx .. NCBI Molecular QTL Browser (ref) .. SCAN (tutorial) .. PheGenI .. eQTL Databases  

eQTL Resources @ Pritchard Lab (browser) .. Blood eQTL Browser .. eQTL Catalog (NESDA/NTR) (ref) .. reQTL (ref)

CAGE eQTL Browser (ref)   ImmunPop eQTL Browser (ref)   GWAS2Genes (ref)    GEUVADIS/1KG (ref; data download)

 mQTLdb (ref) .. HSM (Haplotype-specific Methylation-associated SNPs) (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)

DIVAN (ref)

Obsolete: BIOS QTL Browser (ref1 / ref2) .. e/meQTL .. seeQTL (ref)

 

Splice Site Analysis and ssSNPs

regSNPs-splicing (ref)   dbNSFP (ref)

AS-ALPS (ref)    NNSplice (splice site prediction on genomic sequence)    Human Splicing Finder    Splice-Net  

Splice Disruption Model SNPs @ GTEx

Obsolete ones: ssSNPTarget (ref) .. AASsites (ref)

 

Coding SNP Annotation

genome Aggregation (gnomAD) Browser (formerly ExAc Browser) (ref)

MISCAST (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

OpenTargets PostGWAS   Mastermind (ref)   VariED (ref)   LDtrait (ref)   PhenoScanner (manual / ref

CTG postGWAS: Browser & Virtual Lab (ref)

 GWASdb v2 (JJ Wang Lab)   GWAS Catalog (NHGRI-EBI) (ref)   NCBI GAPplus   GWASKB (ref)  GWAS Central   HuGE Navigator

 GRASP (ref / overview / user guide)   GWAS4D (ref / help)    FUMA GWAS (ref)  LocusZoom (ref)

GWAS-ROCS (ref)    Cancer PRSweb (ref)

HaploReg v4 (ref)    RegulomeDB (GWAS)

  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)

Breast Cancer GWAS: GAME-ON   CGEMS   (KM Plotter)  Human Protein Atlas KM Plotter - Search (ref

GeneAtlas (UK Biobank)   GeneAtlas/PheWAS   PheWeb (UK Biobank) (unpublished)

  Metabolomics GWAS    PGWAS: Proteomics GWAS (ref)

eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual)

humanbase (module/GWAS)

GWAS Summary Results: EBI GWAS Catalog   GRASP

obsolete: MR-Base (ref1 / ref2)   HESS: Heritability Estimation from Summary Statistics of GWAS (ref)   PheWAS Catalog   WGAviewer (ref)   GWATCH (ref)    

 

Epigenetics

BioTools: Epigenetics    EpiGenie Epigenetics Tools   EpiMap / Browser (ref)

NIH RoadMap Epigenomic Browser (tutorial / cell types)   WashU EpiGenome   Human Epigenome Atlas   NCBI Epigenomics (help)  

Int Hum Epigenet Cons (IHEC)   IHEC Data Portal  

EpiRegNet @ JJ Wang Labs

HEDD (Human Epigenetic Drug Database) (ref)

CpG sites list

 

Chromatin Features Databases

BioTools: Chromatin

HEDD (Human Enhancer Disease Database) (ref)   DiseaseEnhancer (Disease-associated enhancers) (ref)   GeneHancer (ref)

SlideBase (FANTOM Enhancers) (tutorial)    EpiRegio (ref / documentation)    epiTAD (ref)

Cistrome DB (for chromatin features) (ref)   NHGRI HistoneDB v.2 (ref

3DIV (3D-genome Interaction Viewer and Database) (ref / tutorial)  

3D Genome Browsers:  Yue Lab (ref / tutorial)    HUGIn (ref / tutorial)    3DGB/McGill (ref)    3Disease Browser (ref / tutorial)

 4D Genome (ref)   3CDB (ref)   CCSI/obsolete (ref)

Human Histone Modification Database (HHMD) (ref)

 

ncRNA (microRNA/lncRNA) & Pseudogene Resources

BioTools: microRNA   BioTools: lncRNA / BioTools: lincRNA   BioTools: ncRNA     

NONCODE (ref)   NPInter v3 (ref)   ncRNA Databases Resource (NRDR)   ChIPBase (ref)

 miRBase   miRDB   mrSNP   TargetScan   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)   miRCancer   OncomiRDB (ref)   HOCTAR (refFAME (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

lncRNAKB (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 (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)

Database of CpG Islands

lnCaNet Database (lncRNA-Cancer co-expression database) (ref)   lncRNA-SNP db (ref)   LncVar (ref)

lncScape (Hematopoietic lineage and leukemia lncRNA expression atlas) (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)

Rfam (ncRNA families)

lncRNome/Obsolete (ref)   lncRNA2Target/Obsolete (ref)   lncRNA2Funxtion/Obsolete (ref)

lncReg/Obsolete (ref)   lncRNAtor/Obsolete (ref)   Co-LncRNA/Obsolete (ref)   TF2LncRNA/Obsolete (ref)

LincSNP v2/Obsolete (ref)   decodeRNA/Obsolete (ref)

 

Gene Expression (incl. cancer) & Cancer Informatics

Cancer Cell Line Encyclopedia / CCLE (ref)   Human Protein Atlas: Cancer

   RNA-seq Atlas (ref)   Expression Atlas (ref)   lnCaNet Database (ref)   PanglaoDB (ref)

TSEA (Tissue Specific Expression Analysis) (ref)

PancanQTL (ref)    Pancan meQTL (ref)

ORGANize (linking genes to the organs they affect) (ref / help)  

SAGD (sex-associated gene database from transcriptomes) (ref)

Gene Enrichment Profiler (ref)

Brain: Cortecon (ref)   BrainSpan (ref / help)

 & 

Cancer Genomics and Epidemiology Navigator (CGEN)

(KM Plotter)  Human Protein Atlas KM Plotter (ref)

BloodSpot (AML) (ref)

Databases for Cancer Genomics (Table 2 in Chin, 2011)

UCSC Xena Browser    ActiveDriverDB (variation in post-translational modification sites) (ref)

 

Transcription Factor Binding Site Search

GVATdb (Genetic Variants Allelic TF Binding Database) (ref)

 TransFac  TFBS Search (Qiagen)  TFBS Mapper (refTFBIND  MFold   JasPar  PAZAR  SNP@llincRNA TFBS (ref)

 Swiss Regulon (by TF Name)   AR Target Gene Dbase   TESS-discontinued  

CTCFBSDB v2 (ref)

 

Cancer Somatic Mutations

 COSMIC (somatic mutations in cancer) .. COSMIC Browser .. ICGC Data Portal .. NCBI Cancer Genome Anatomy Project .. cBioPortal 

HotSpotAnnotations (ref)

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)    GSEA/MSigDB    GSAn (ref)   ConsensusPath (CPdB) (ref / protocol)   Pathway Commons (guide / primer)

  DAVID (ref / tutorial / protocol)   SSEA (ref)   g:Profiler (ref / protocol)

 Cytoscape    Disease Connect    ToppGene (ref)    Panda (ref / video tutorial)   WebGestalt (ref)

UniHi   Reactome (user guide)   Reactome Pathway Browser   BioSystems   Pathway Searcher   KEGG 

 Gene Ontology    GeneSetDB    GeneFamilies            

GSEA & GSEA-SNP   GIANT (Gene Networks in Tissues; Ref)   Onto-Tools (user guide)

FUMA-GENE2FUNC

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

The Genome Network Project (GNP)   Genetic Network Analysis Tool (GNAT) (ref)

GeneNetwork-UT / GN2 (co-expression) (ref)    Human Gene Correlation Analysis (co-expression) (ref)   CORD (ref) (co-regulation) 

GLITTER (tissue-specific coexpression) (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)

Ingenuity Target Analysis  

 

Gene Ontology

QuickGO (ontology) .. Gene Ontology (AmiGO browser)

GeneNetwork-UCMG (function, expression and co-expression) .. GeneNetwork-UT

Harmonizome (ref)

 

Immunoinformatics

 MHC Haplotype Project   dbMHC (search)

IPD-IMGT/HLA (ref)    MHCcluster (ref)   Immune Epitope Database (IEDB) (video tutorials/ref)

Registry of Antibody-Defined HLA Epitopes (ref)    HLA Epitopes @ Allele Frequencies.Net (ref)

IMGT/HLA Allele Query    IGDAWG (Global Frequency Map Browser)   PyPop Population Data

 ImmPort (tutorial)   ImmVar   ImmunoBase (browser)   ImmuNet (ref)   ImmuneCellScience (ref)   ImmGene-Mouse (ref / video)

FineMapping / PICS (ref)    SNP2HLA (Imputation of Amino Acid Polymorphisms in HLA) (ref / manual)

BIGDAWG Case-Control HLA Data Analysis (ref)   HLA-NET GENE[RATE] Tools (publications)

HLA-NET: Charts & Maps

The SysteMHC Atlas project: MS-generated immunopeptidomic data (ref)

HLA-MA (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

 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

NAR Database: Disease

dSysMap (ref / tutorial)   Disease Connect   CoreMine   GWASdb v2   Phenolyzer (ref / tutorial)   PhenoPred   SNPs3D  DisGeNET (ref)

FANTOM CAT Traits Database    3Disease Browser (ref / tutorial)    eDGAR (Disease-Gene Associations) (ref / tutorial)

Comparative Toxicogenomics Database (CTD) 

SZGR (ref)    SZDB Database (ref)   Brain xQTL Serve (ref)   Alzheimer Disease Gene Exp Browser (ref)   Type 2 Diabetes  

 

Various Other Resources

Gene Prediction Tools

 AUGUSTUS Gene Prediction Tool (tutorial)   Gene Prediction 

 

STR Database

 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  

JJ Wang Lab   Cui Lab 

 

Search Templates

(use these static URLs for quick searches by changing the indicated identifier to yours in the address line)

Gene (Gene Name1/Human)  Gene (Gene Name2)  Gene (GeneID)

dbSNP (GeneID)   dbSNP (rs#)   Ensembl (rs#)   SNiPA (rs#)

GWAS Cat (EBI) (rs#)  PhenoScanner (rs#)   GeneAtlas-PheWAS (UK Biobank) (rs#)

 PheGenI (rs#)   dbGAP (rs#)   GWAS Central (rs#)   Super-EnhancerDB (rs#)   GTEx (rs#)

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)

Variation Viewer (geneName)   rVarBase (rs#)   HaploReg v4 (rs#)  Omni (rs#)  HSM (rs#)

 

Vega / Ensembl (Gene Name)  Ensembl (rs#)   SNPedia (rs#)

RegulomeDB (chr#/nt#)   OpenSNP (rs#)   SNPDelScore (rs#): Restful (API)

ENCODE Regulatory Elements DB (Gene Name)    GenCode - Alternative Splicing Variants (Gene Name)

 Expression Atlas (Gene Name)   Protein Atlas (Gene Name)   

Virtual 4C (rsID and GM12878)

LDAssoc / LDPair (LD between two SNPs in EUR populations)  

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)  

Amino Acids   Genetic Code   Ambiguity (Mixed Base) Codes

 BioCompare

 

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

Applied Bioinformatics Course (ABC) (ref)

Bioinformatics Training and Services (BITS) - Exercises

Tutorials: NCBI  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)

 

HGNC Human Genetic Nomenclature Guide

Mouse Genetic Nomenclature

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

Teaching Statistics with R (CRAN Task View)  

 

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)

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)  

GenomicFeatures (vignette)   GenomicRanges (vignette1 & 2HelloRanges (tutorial)  

GSOAP (visualization of gene set over-representation analysis) (ref)

gprofiler2 (ref / vignette) DOSE (ref / vignette)   clusterProfiler/GSEA (ref)    ReactomePA

 deTS (ref / GitHub)    disgenet2r (ref / GitHub) CONQUER (ref)

BioMedR (ref / vignette / GitHub)    HPAanalyze (ref / GitHub)

F1000Research: Bioconductor

Obsolete: NCBI2R (GitHub)

 

LINKS

Links to Bioinformatics Tools @ ABC

Bioinformatics.ca

OMICSTools     Dataset2Tools (Tools) (ref)     BioTools

Online Bioinformatics Resources Collection

 

Mehmet Tevfik DORAK, MD, PhD

 

Genome Biology     Genetics     Biostatistics    R    Population Genetics    Genetic Epidemiology    HLA     MHC     Homepage

 

5 April 2021