Difference between revisions of "Web Resources"
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| − | == | + | == Google DataSet Search Engine == |
| − | *[ | + | *[https://toolbox.google.com/datasetsearch Google Dataset Search] |
| − | + | == Gene/Genome Annotations == | |
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*[http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi CCDS] The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation | *[http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi CCDS] The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation | ||
*[http://www.gencodegenes.org/ GENCODE] The Encyclopedia of Genes | *[http://www.gencodegenes.org/ GENCODE] The Encyclopedia of Genes | ||
| − | *[ | + | *[https://metascape.org/ Metasape] Gene annotation and Enrichment analysis resource by NIH |
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| − | == | + | == Variome Resources == |
| − | + | - Variation DBs | |
| − | *[http:// | + | *[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals |
| − | + | *[http://www.1000genomes.org/ 1000 Genome Project] Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations | |
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| − | *[http://www.1000genomes.org/ 1000 | + | |
*[http://www.uk10k.org/ UK10K] Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England | *[http://www.uk10k.org/ UK10K] Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England | ||
*[http://www.genomicsengland.co.uk/ Genomics England] Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer. | *[http://www.genomicsengland.co.uk/ Genomics England] Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer. | ||
| − | + | *[http://www.discovehrshare.com/ DiscovEHR] Collaboration between the Regeneron Genetics Center (WES) and Geisinger Health System (EHR) provides the vcf by 50,000 MyCode participants | |
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*[http://www.ebi.ac.uk/eva/ European Variation Archive] Most comprehensive and organized by studies (include Clinical variants) | *[http://www.ebi.ac.uk/eva/ European Variation Archive] Most comprehensive and organized by studies (include Clinical variants) | ||
*[http://www.ncbi.nlm.nih.gov/variation/ NCBI Variation] Variation DBs (dbSNP, dbVar, dbGaP, ClinVar) | *[http://www.ncbi.nlm.nih.gov/variation/ NCBI Variation] Variation DBs (dbSNP, dbVar, dbGaP, ClinVar) | ||
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*[http://ijgvd.megabank.tohoku.ac.jp/ iJGVD] Integrative Japanese Genome Variation Database | *[http://ijgvd.megabank.tohoku.ac.jp/ iJGVD] Integrative Japanese Genome Variation Database | ||
*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation | *[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation | ||
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| − | + | - Functional significance of variants | |
| + | *[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration) | ||
| + | *[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration) | ||
| + | *[https://www.sanger.ac.uk/sanger/StatGen_Gwava GWAVA: Genome Wide Annotation of VAriants] a tool which aims to predict the functional impact of non-coding genetic variants (human only, supervised integration) | ||
*[http://asia.ensembl.org/info/docs/variation/vep/index.html VEP] Variant Effect Predictor by EBI (very easy to install and use) | *[http://asia.ensembl.org/info/docs/variation/vep/index.html VEP] Variant Effect Predictor by EBI (very easy to install and use) | ||
*[http://bg.upf.edu/condel/home Condel] Variant effect score by integration of SIFT, Polyphen2, Massessor, MAPP, Logre | *[http://bg.upf.edu/condel/home Condel] Variant effect score by integration of SIFT, Polyphen2, Massessor, MAPP, Logre | ||
*[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)] | *[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)] | ||
| − | *[http:// | + | *[http://sift.bii.a-star.edu.sg/sift4g/ SIFT4G] SIFT for many genomes |
| − | *[http:// | + | *[http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2 (Polymorphism Phenotyping v2)] for human coding region only |
*[http://www.regulomedb.org/ RegulomeDB] Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab) | *[http://www.regulomedb.org/ RegulomeDB] Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab) | ||
*[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab) | *[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab) | ||
| − | == | + | == Phenome/Diseasome Resources == |
| + | - Human Disease DBs | ||
| + | *[http://www.disgenet.org/web/DisGeNET DisGeNET] MetaDB for disease genes and variants (very comprehensive and open license) | ||
| + | *[https://www.opentargets.org/ Open Targets] Another very comprehensive DB for disease target (mostly protein-coding genes) and related evidence | ||
| + | *[http://denovo-db.gs.washington.edu/denovo-db/ denovo-db] a compendium of human de novo variants | ||
| + | *[http://diseases.jensenlab.org/ DISEASES] gene-disease association from text mining (GHR, Uniprot, textmining) | ||
| + | *[https://ghr.nlm.nih.gov/ GHR] Genetics Home Reference (by NCBI) | ||
| + | *[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map | ||
| + | *[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology] | ||
| + | *[http://www.omim.org/ OMIM] Human disease DB (needs License to distribute) | ||
| + | *[http://www.orphadata.org OrphaData] Open database for rare diseases and orphan drug (by Orphanet) | ||
| + | *[http://geneticassociationdb.nih.gov/ GAD] Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies). | ||
| + | *[http://www.nlm.nih.gov/research/umls/ UMLS] Unified Medical Language Systems | ||
| + | *[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO | ||
| + | *[http://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships | ||
| + | *[http://genomernai.de/GenomeRNAi/ GenomeRNAi] v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets | ||
| + | *[http://ogeedb.embl.de OGEE] Online GEne Essentiality database | ||
| + | *[http://www.informatics.jax.org/humanDisease.shtml Human-Mouse Disease Connection] a part of MGI | ||
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| + | - QTL depositories | ||
| + | *[https://www.gtexportal.org/home/ GTEx Portal] eQTL for ~50 different tissue types in humans | ||
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| + | - GWAS resources | ||
| + | *[https://www.covid19hg.org/results/ COVID-19 Host Genetics Inititative]COVID-19 GWAS regulsts | ||
| + | *[https://atlas.ctglab.nl/ GWAS ATLAS] Atlas of GWAS Summary Statistics (most comprehensive!) | ||
| + | *[http://www.ebi.ac.uk/gwas/ GWAS catalog] Disease-associated variants; Now providing GWAS summary stat data | ||
| + | *[http://geneatlas.roslin.ed.ac.uk/ GeneATLAS] GWAS for ~780 traits using 452,264 UK Biobank White British individuals | ||
| + | *[http://www.ncbi.nlm.nih.gov/gap/phegeni PheGenI] Phenotype-Genotype Integrator: For a query trait, it return GWAS loci collected from all available data resources (very convenient to make a single GWAS data set for each trait) | ||
| + | *[http://ldsc.broadinstitute.org/ldhub/ LDHUB] a centralized database of summary-level GWAS results | ||
| + | *[http://apps.nhlbi.nih.gov/Grasp/ Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP)] Better than GWAS catalog, including eQTL,QTLs | ||
| + | *[http://jjwanglab.org:8080/gwasdb/ GWASdb] includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms | ||
| + | *[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks | ||
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| + | - Genotype raw data depositories | ||
| + | *[http://www.humanfunctionalgenomics.org Human Functional Genomics Project] Raw data are available from [https://hfgp.bbmri.nl/ BBMRI-NL data infrastructure] | ||
| + | *[http://www.ukbiobank.ac.uk/ UK Biobank] Genotype and extensive phenotype data for ~500k UK people | ||
*[https://www.ebi.ac.uk/ega/ European Genome-phenome Archive(EGA)] Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis | *[https://www.ebi.ac.uk/ega/ European Genome-phenome Archive(EGA)] Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis | ||
*[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...) | *[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...) | ||
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| + | - Clinical/Disease variant databases | ||
| + | *[http://research.nhgri.nih.gov/CGD/ CGD] Clinical Genomic Database | ||
| + | *[http://www.hgmd.org/ HGMD] The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.) | ||
| + | *[http://www.ncbi.nlm.nih.gov/omim OMIM] Germline mutations for genetic diseases | ||
| + | *[http://rcgdb.bioinf.uni-sb.de/MutomeWeb/ Roche Cancer Genome Database (RCGDB)] Germline/somatic mutations for cancer collected from diverse resourses (not downloadable) | ||
| + | *[http://bioinf.uta.fi/base_root/ IDbase] Human Immunodeficiency-causing mutation database | ||
*[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS) | *[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS) | ||
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*[http://www.nature.com/icogs/ COGS nature resources] CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers. | *[http://www.nature.com/icogs/ COGS nature resources] CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers. | ||
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*[http://www.personalgenomes.org/ Personal Genome Project] | *[http://www.personalgenomes.org/ Personal Genome Project] | ||
| − | + | *[https://decipher.sanger.ac.uk/ DECIPHER] Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research) | |
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| − | == | + | == Interactome, Pathway/Signature Resources == |
| − | *[ | + | - Interactome DBs |
| − | *[http:// | + | *[https://irefindex.vib.be/wiki/index.php/iRefIndex iRefIndex] provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI, Reactome, VirHostnet, and QuickGO. |
| + | *[http://string-db.org/ STRING] Known and predicted PPI | ||
| + | *[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions | ||
| − | + | - Pathway DBs | |
| + | *[http://pathguide.org/ Pathguide.org] A very comprehensive list of pathway and network databases | ||
*[http://www.geneontology.org/ Gene Ontology] by Gene Ontology Consortium | *[http://www.geneontology.org/ Gene Ontology] by Gene Ontology Consortium | ||
*[http://www.genome.jp/kegg/ KEGG] pathways and many more | *[http://www.genome.jp/kegg/ KEGG] pathways and many more | ||
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*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes | *[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes | ||
*[http://www.netpath.org/ NetPath] A database for signaling pathways (cancer/immune signaling pathways) | *[http://www.netpath.org/ NetPath] A database for signaling pathways (cancer/immune signaling pathways) | ||
| + | *[http://signor.uniroma2.it/index.jsp SIGNOR] 11000 manually-annotated causal relationships between proteins that participate in signal transduction | ||
*[http://www.ebi.ac.uk/GOA/ UniProt-GOA] by EBI (support multi-species annotation) | *[http://www.ebi.ac.uk/GOA/ UniProt-GOA] by EBI (support multi-species annotation) | ||
*[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc) | *[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc) | ||
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| − | + | - Signature Gene Set DBs | |
| − | + | *[http://software.broadinstitute.org/gsea/msigdb MsigDB] License required for redistribution | |
| − | *[http:// | + | *[http://www.genesigdb.org/genesigdb/ GeneSigDB] Manually curated gene sets from Pubmed literature |
| − | *[http://www. | + | *[https://www.immunespace.org/announcements/home/thread.view?rowId=50 ImmnuneSigDB] Compendium of immune signatures (now available from MsigDB) |
| − | *[ | + | *[http://biocc.hrbmu.edu.cn/CancerSEA/goDownload CancerSEA] which provides 14 signature profiles for characterization of cancer cells |
| − | + | *[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis | |
| − | + | *[http://amp.pharm.mssm.edu/L1000CDS2/help/ L1000CDS2] Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method | |
| − | *[http:// | + | *[http://amp.pharm.mssm.edu/creeds/ CREEDS] CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method |
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| − | == | + | == Regulome Resources == |
| − | - | + | - TF and motif DB |
| + | *[http://humantfs.ccbr.utoronto.ca/ The Human Transcription Factors] 2765 putative TFs and 1639 confident TFs by manual curation | ||
*[http://cisbp.ccbr.utoronto.ca/ CIS-BP (Catalog of Inferred Sequence Binding Preferences)] >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as [http://autosome.ru/HOCOMOCO/ HOCOMOCO] [http://jaspar.genereg.net JASPAR] [http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] [http://www.gene-regulation.com/pub/databases.html TRANSFAC] | *[http://cisbp.ccbr.utoronto.ca/ CIS-BP (Catalog of Inferred Sequence Binding Preferences)] >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as [http://autosome.ru/HOCOMOCO/ HOCOMOCO] [http://jaspar.genereg.net JASPAR] [http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] [http://www.gene-regulation.com/pub/databases.html TRANSFAC] | ||
| − | - | + | - Epigenomics Consortium projects |
| − | *[http:// | + | *[https://www.encodeproject.org/ ENCODE] Encyclopedia of DNA Elements project portal |
| + | *[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home | ||
| + | *[http://ihec-epigenomes.org/ International Human Epigenome Consortium (IHEC)] The umbrella organization for international epigenomic efforts | ||
| + | *[http://www.4dnucleome.org/ 4D Nucleome] To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension) | ||
| − | - | + | - Promoter DB |
| − | *[http:// | + | *[http://epd.vital-it.ch/ EPD] Eukaryotic Promoter Database; Databases of experimentally validated (by either publication or in-house assay) promoters in various organisms |
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| − | - | + | - Enhancer DB |
| − | *[http:// | + | *[http://enhanceratlas.org/ Enhancer Atlas] Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues) |
| + | *[http://bioinfo.au.tsinghua.edu.cn/dbsuper/ dbSUPER] contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types | ||
| + | *[http://zdzlab.einstein.yu.edu/1/hedd.php HEDD] Human Enhancer Disease Database (~2.8M enhancers from ENCODE, FANTOM5, RoadMap and annotations for disease, target, variant, conservation) | ||
| + | *[http://biocc.hrbmu.edu.cn/DiseaseEnhancer/ DiseaseEnhancer] manual curation of disease-associated enhancers | ||
| − | - | + | - Transcriptional Start Site (TSS) DB |
| − | + | *[http://dbtss.hgc.jp/ DBTTS] contains 491 million TSS tag sequences for 20 tissues and 7 cell cultures in human and mouse | |
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| − | - | + | - Chip-seq/DNase-seq DB |
| − | *[http:// | + | *[http://cistrome.org Cistrome DB] the most comprehensive DB for Chip-seq and DNase-seq data |
| − | + | - Enhancer-Promoter Interaction DB | |
| − | -microRNA list and expression atlas | + | *[http://yiplab.cse.cuhk.edu.hk/jeme/ JEME] Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines |
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| + | - microRNA list and expression atlas | ||
*[http://mirbase.org// miRBase] miRNA database by Manchester University | *[http://mirbase.org// miRBase] miRNA database by Manchester University | ||
*[http://www.microrna.org microRNA.org] download miRNA expression atlas for human, mouse, rat | *[http://www.microrna.org microRNA.org] download miRNA expression atlas for human, mouse, rat | ||
| − | -microRNA-target links (Gold standard) | + | *[https://bioconductor.org/packages/devel/data/experiment/html/microRNAome.html microRNAome] microRNA RNA-seq based atlas for 46 primary cell types and 42 cancer or immortalized cell lines |
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| + | - microRNA-target links (Gold standard) | ||
*[http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2 miRWalk2.0] Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets | *[http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2 miRWalk2.0] Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets | ||
| − | *[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase] | + | *[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase] Experimental-based microRNA-target links (most popular) |
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| − | + | - microRNA-disease | |
| − | + | *[http://202.38.126.151/hmdd/tools/hmdd2.html Human microRNA Disease Database(HMDD)] Manually curated microRNA-disease links (most comprehensive) | |
| − | + | *[http://mips.helmholtz-muenchen.de/phenomir/ PhenomiR] DB for dysregulated miRNA in diseases | |
| − | -microRNA-disease | + | *[http://www.picb.ac.cn/dbDEMC/ dbDEMC] DB for dysregulated miRNA in Cancer |
| − | *[http://202.38.126.151/hmdd/tools/hmdd2.html Human microRNA Disease Database(HMDD)] Manually curated microRNA-disease links | + | |
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*[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments... | *[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments... | ||
| − | -Target | + | |
| − | *[http:// | + | - miRNA Target predictions |
| − | + | *[http://ophid.utoronto.ca/mirDIP/ mirDIP] >150M human miRNA-target predictions collected from 30 resources with integrative score | |
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| − | -CLIP-seq database | + | - CLIP-seq database |
*[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data | *[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data | ||
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| − | + | - lncRNA Resources | |
| + | *[http://fantom.gsc.riken.jp/cat/ FANTOM-CAT] An atlas of human long non-coding RNAs with accurate 5' ends | ||
*[http://www.noncode.org/ NONCODE] Integrative annotation of long noncoding RNAs | *[http://www.noncode.org/ NONCODE] Integrative annotation of long noncoding RNAs | ||
*[http://www.lncrnadb.org/ lncRNAdb] a reference DB for long noncoding RNAs | *[http://www.lncrnadb.org/ lncRNAdb] a reference DB for long noncoding RNAs | ||
| + | *[http://rth.dk/resources/rain/ RAIN] RNA–protein Association and Interaction Networks [http://benasque.org/2015rna/talks_contr/283_20150728-RAIN-Benasque.pdf Intro to RAIN] | ||
*[http://www.bioinfo.org/NPInter/ NPInter] ncRNA interaction database (ncRNA and other molecules) | *[http://www.bioinfo.org/NPInter/ NPInter] ncRNA interaction database (ncRNA and other molecules) | ||
| + | *[http://www.rna-society.org/raid/ RAID] RNA-associated interaction DB (very comprehensive) | ||
*[http://cmbi.bjmu.edu.cn/lncrnadisease LncRNADisease] a DB for lncRNA associated diseases | *[http://cmbi.bjmu.edu.cn/lncrnadisease LncRNADisease] a DB for lncRNA associated diseases | ||
*[http://www.bioinfo.org/ncfans/ ncFANs] a web server for functional annotation of ncRNA | *[http://www.bioinfo.org/ncfans/ ncFANs] a web server for functional annotation of ncRNA | ||
| + | *[http://210.46.80.146/lincsnp/ LincSNP] a DB of disease-associated SNP in human lncRNA and their TFBS | ||
| + | *[http://lulab.life.tsinghua.edu.cn/postar/ POSTAR] a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods) | ||
| − | == | + | == Single Cell Analysis Resources == |
| − | *[ | + | - Spatial Omics Resources |
| − | *[ | + | *[https://github.com/crazyhottommy/awesome_spatial_omics awesome_spatial_omics] |
| − | *[https:// | + | - Human Cell Atlas |
| − | *[ | + | *[https://www.humancellatlas.org/ HCA] |
| − | *[ | + | *[https://chanzuckerberg.com/science/programs-resources/humancellatlas/ Chan Zukerburg Initiative HCA seed networks] |
| − | *[ | + | *[https://www.covid19cellatlas.org/ COVID-19 Cell Atlas] Data portal by HCA |
| − | *[ | + | - scRNA-seq data analysis resources |
| − | *[http:// | + | *[https://satijalab.org/seurat/ Seurat] The package for scRNA-seq data analysis |
| − | *[http:// | + | *[https://velocyto.org Velocyto] RNA Velocity analysis with steady-state model |
| − | *[http:// | + | *[https://scvelo.org scVelo] Generalized RNA Velocity analysis through dynamic modeling |
| − | *[ | + | *[https://www.sanger.ac.uk/science/tools/scrna-seq-analysis-course scRNA-seq analysis course by Sanger] |
| + | *[https://www.cellphonedb.org/ CellPhoneDB] A repository of curated receptors, ligands and their interactions. | ||
| + | *[https://github.com/seandavi/awesome-single-cell Awesome single cell] | ||
| + | *[https://www.scrna-tools.org/ scRNA-tools DB] | ||
| + | - Depositories for scRNA-seq data | ||
| + | *[https://portals.broadinstitute.org/single_cell Single Cell Portal] scRNA-seq database by Broad Institute | ||
| + | *[https://bioinfo.uth.edu/scrnaseqdb/ scRNASeqDB] scRNA-seq database by UTHSC | ||
| + | *[http://imlspenticton.uzh.ch:3838/conquer/ conquer] A repository of consistently processed, analysis-ready single-cell RNA-seq data sets | ||
| + | *[http://jinglebells.bgu.ac.il/ Jinglebells] A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level | ||
| + | *[http://single-cell.clst.riken.jp/ SCPortalen] human and mouse single-cell centric database | ||
| + | *[https://support.10xgenomics.com/single-cell-gene-expression/datasets 10X Genomics Datasets] by 10X Genomics | ||
| − | == | + | ==Chemical Biology and Drug Research Resources== |
| − | - | + | - Prioritizing Drugs for target gene regulation |
| − | + | *[https://maayanlab.cloud/DGB/ Drug Gene Budger] based on LINCS, GEO, CMAP data [https://pubmed.ncbi.nlm.nih.gov/30169739/ DGB reference] | |
| − | *[https:// | + | - Drug and Bioactive chemical DBs |
| − | + | *[https://clue.io/repurposing Drug Repurposing Hub] a best-in-class drug screening collection of >3,000 clinical drugs and their annotation (structure, MoA, protein targets) | |
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*[http://drugable.com/ Drugable.com] by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model | *[http://drugable.com/ Drugable.com] by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model | ||
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] A DB contains drug structure and function by NCBI | *[http://pubchem.ncbi.nlm.nih.gov/ PubChem] A DB contains drug structure and function by NCBI | ||
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*[http://bioinf.charite.de/superdrug/ SuperDrug] A DB contains 3D-structures of drugs | *[http://bioinf.charite.de/superdrug/ SuperDrug] A DB contains 3D-structures of drugs | ||
| − | + | - Clinical Trial Information | |
| − | *[http:// | + | *[http://clinicaltrials.gov/ ClinicalTrials.gov] DB for clinical trials conducted around the world |
| + | |||
| + | - Drug Target DBs | ||
| + | *[https://www.dgidb.org/ DGIdb] An integrated Drug-Gene Interaction DB | ||
| + | *[https://www.ncbi.nlm.nih.gov/pubmed/27910877 A curated drug-target map] by curation of [https://www.ebi.ac.uk/chembl/ ChEMBL database], [http://drugcentral.org/ DrugCentral database], [https://cansar.icr.ac.uk/ canSAR knowledge base] (Gold Standard drug-target) | ||
*[http://www.genome.jp/kegg/drug/ KEGG DRUG] contains information about only approved drugs | *[http://www.genome.jp/kegg/drug/ KEGG DRUG] contains information about only approved drugs | ||
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction | *[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction | ||
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*[http://www.guidetopharmacology.org/ IUPHAR/BPS Guide to Pharmacology] A DB of in-depth information of drug targets and ligands | *[http://www.guidetopharmacology.org/ IUPHAR/BPS Guide to Pharmacology] A DB of in-depth information of drug targets and ligands | ||
*[http://pdsp.med.unc.edu/kidb.php PDSP Ki DB] data warehouse for published and internally-derived Ki, or affinity of drugs at targets | *[http://pdsp.med.unc.edu/kidb.php PDSP Ki DB] data warehouse for published and internally-derived Ki, or affinity of drugs at targets | ||
| − | |||
| − | + | - Drug signature, Pharmacogenomics, Toxicogenomics DBs | |
| − | *[http:// | + | *[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis |
| + | *[https://clue.io/ CLUE] The expanded CMap including 1.3M L1000 profiles for 27,927 perturbagens (476,251 expressions) | ||
| + | *[http://www.ilincs.org iLINCS] Integrated System to Analyze LINCS and other data | ||
| + | *[https://www.broadinstitute.org/cmap/ Connectivity Map (CMap)] 7,000 expression profiles representing 1,309 compounds | ||
*[http://ctd.mdibl.org/ The Comparative Toxicogenomics database(CTD)] The major DB of chemical-disease links from literature curation | *[http://ctd.mdibl.org/ The Comparative Toxicogenomics database(CTD)] The major DB of chemical-disease links from literature curation | ||
*[http://toxico.nibio.go.jp/english/index.html TG-GATE] Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans | *[http://toxico.nibio.go.jp/english/index.html TG-GATE] Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans | ||
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*[http://sideeffects.embl.de/ SIDER] Side Effect Resource | *[http://sideeffects.embl.de/ SIDER] Side Effect Resource | ||
| − | == Cancer | + | - Drug-Gene Interaction DBs |
| − | - | + | *[http://mosaic.cs.umn.edu/ MOSAIC] Chemical-genetic interactions in Yeast (cover >13000 compounds) |
| − | *[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC | + | |
| − | *[http://cancer.sanger.ac.uk/cancergenome/projects/census/ CGC | + | == Cancer Biology Resources == |
| − | + | - Cancer Somatic Mutations DBs | |
| − | *[https://www. | + | *[https://search.cancervariants.org/ meta-knowledgebase of somatic variants] Harmonized integration of Cancer Genome Interpreter, CIVIC, JAX-CKB, MolecularMatch, OncoKB, PMKB |
| − | *[http:// | + | *[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC(The Catalog Of Somatic Mutations In Cancer)] By Sanger with expert curation |
| − | *[https:// | + | *[http://docm.info DoCM] A database of functional variants validated in cancer |
| − | *[ | + | *[http://civicdb.org CIViC] A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer |
| − | *[https://dcc.icgc.org/ ICGC data portal] raw data from ICGC and TCGA | + | |
| − | *[ | + | - Cancer Somatic Mutation Visualization |
| − | -Data | + | *[https://pecan.stjude.cloud/proteinpaint Proteinpaint] Exploring genomic alteration in pediatric cancer |
| − | *[https://www.synapse.org/#!Synapse: | + | |
| − | -Cancer Genomics Data Analysis | + | - Cancer Gene DBs |
| − | *[http:// | + | *[http://cancer.sanger.ac.uk/cancergenome/projects/census/ CGC(Cancer Gene Census}] A catalog of genes with mutations that are causally implicated in cancer (by COSMIC) |
| − | *[http:// | + | *[https://www.ncbi.nlm.nih.gov/pubmed/23539594 125 mutation-based drivers] see Supple TableS2A (71 TSG and 54 OG by 20/20 rule) |
| − | + | *[https://bioinfo.uth.edu/TSGene/ TSGene] Literature-curated 1217 human TSGs (1018 protein-coding and 199 non-coding genes) and 320 protein-coding oncogenes | |
| − | *[http:// | + | *[http://ccgd-starrlab.oit.umn.edu CCGD(Candidate Cancer Gene Database)]A database of cancer driver genes from transposon-based forward genetic screens in mice |
| − | *[http:// | + | *[https://www.nature.com/articles/nrc2771 77 Cancer Genes by amplification and overexpression] see Supple TableS2 |
| − | *[ | + | *[http://ncg.kcl.ac.uk/ NCG(The Network of Cancer Genes)] (~500) CGC + (~1000) Candidate genes from Panel Seq, WES, WGS studies |
| − | *[http:// | + | |
| − | *[http://www. | + | - Cancer Genomics Research Gateway |
| − | *[ | + | *[https://gdc.cancer.gov/ NCI Genomic Data Commons] GDC provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies. |
| − | - | + | *[https://dcc.icgc.org/ ICGC data portal] raw data from '''ICGC''' and '''TCGA''' |
| + | *[https://ocg.cancer.gov/programs/target TARGET(Therapeutically Applicable Research To Generate Effective Treatments)] '''Childhood Cancer''' Genome Project by NCI | ||
| + | *[https://www.pedpancan.com/pedpancan/ PedPanCan(A Pan-Cancer Study of '''Childhood Cancers''')] by Multi-Institutes including St. Jude Children's Research Hospital | ||
| + | *[https://ocg.cancer.gov/ NCI Office of Cancer Genomics] OCG is dedicated to supporting cancer genomics research by sharing molecular data from its programs to enhance understanding of cancer. | ||
| + | *[https://ocg.cancer.gov/programs/ctd2/data-portal CTD2 data portal] Data Portal of [https://ocg.cancer.gov/programs/ctd2/overview Cancer Target Discovery and Development] program which strives to functionally validate discoveries from large-scale genomic initiatives. | ||
| + | *[https://www.synapse.org/#!Synapse:syn7222066/wiki/405659 Synapse GENIE] The largest public cancer genome data by ACCR (see [http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WJv3szuLSUk ACCR GENIE project]) | ||
| + | *[https://www.broadinstitute.org/software/cprg/ Cancer Program Resource Gateway] by Broad | ||
| + | |||
| + | - Cancer Genomics Data Analysis Cloud Platforms | ||
| + | *[http://xena.ucsc.edu/ UCSC Xena] An online exploration tool for public (TCGA, ICGC and more) and private, multi-omic and clinical/phenotype data | ||
| + | *[http://cgc.systemsbiology.net/ ISB-CGC] Cancer Genomics Cloud by ISB | ||
| + | *[http://mev.tm4.org WebMeV] Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded). | ||
| + | |||
| + | - Tumor Microenvironment Analysis tools | ||
| + | *[https://cistrome.shinyapps.io/timer/ TIMER] Web server for a comprehensive TME analysis | ||
| + | *[http://xcell.ucsf.edu/ xCell] Tumor cellular heterogeneity analysis web server; R package is also available from [https://github.com/dviraran/xCell github] | ||
| + | |||
| + | - Cancer Pharmacogenomics | ||
| + | *[https://pharmacodb.pmgenomics.ca/ PharmacoDB] Integrative database for cancer pharmacogenomics (CCLE, GDSC, CTRP, and more) | ||
| + | *[https://portals.broadinstitute.org/ctrp/ CTRP] The Cancer Therapeutics Response Portal (~550 drugs x ~890 cell lines) | ||
| + | *[http://www.cancerrxgene.org/ Genomics of Drug Sensitivity in Cancer (GDSC)] (~250 drugs x ~1110 cell lines) | ||
| + | *[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] (~20 drugs x ~1060 cell lines) | ||
| + | |||
| + | - Cancer cell essential genes | ||
| + | *[http://genomecrispr.dkfz.de GenomeCRISPR] A database for high-throughput CRISPR/Cas9 screening experiments | ||
| + | *[http://www.broadinstitute.org/achilles Achilles Project] shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8) | ||
*[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines | *[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines | ||
| − | == | + | == Immunogenetics DBs and tools == |
| − | *[ | + | *[https://www.iedb.org/ Immune Epitope Database] The most comprehensive (immunogenic and pathogenic) epitope database |
| − | *[http:// | + | *[http://projects.met-hilab.org/tadb/ TANTIGEN] Tumor T-cell Antigen database (>1000 peptides by literature curation) |
| − | *[ | + | *[https://caped.icp.ucl.ac.be/about Cancer Antigenic Peptide Database] ~400 peptides by literature curation |
| + | |||
| + | == Microbiomics DBs and tools == | ||
| + | - Gut microbial biobank by Automated culturomics | ||
| + | *[http://microbial-culturomics.com/] CAMII biobank | ||
| − | + | - Microbiome Data Analysis Resources | |
| − | - | + | *[https://www.youtube.com/playlist?list=PLOPiWVjg6aTzsA53N19YqJQeZpSCH9QPc Microbiome Discovery] Awesome Lectures by Dan Knight |
| − | *[https://www. | + | |
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*[http://huttenhower.sph.harvard.edu/ Huttenhower Lab] A great resource for analysis tools | *[http://huttenhower.sph.harvard.edu/ Huttenhower Lab] A great resource for analysis tools | ||
| − | *[https:// | + | *[https://hcmph.sph.harvard.edu/ Harvard Chan Microbiome in Public Health Center (HCMPH)] |
| − | + | ||
| − | + | ||
| − | + | - Microbiome Catalogs and Taxonomy | |
| − | *[ | + | *[https://gtdb.ecogenomic.org/ GTDB] BACTERIAL GENOME TAXONOMY DATABASE |
| − | *[ | + | *[https://www.mbiomenet.org/HRGM/ HRGM] Human Reference Gut Microbiome by Yonsei University |
| + | *[https://www.ebi.ac.uk/metagenomics/genomes UHGG] Unified Human Gastrointestinal Genome by EBI | ||
| + | *[http://gmgc.embl.de/ GMGC] Global Microbial Gene Catalog by EMBL | ||
| − | + | -Microbiome-Disease(drug, diet) interaction DBs | |
| − | *[ | + | *[https://disbiome.ugent.be/ Disbiome] Microbe-Disease interactions |
| − | *[http://www. | + | *[http://www.aiddlab.com/MASI/ MASI] Microbe-Drug(Disease, Diet) interactions |
| − | + | *[http://bio-annotation.cn/gutMDisorder/ gutMDisorder] Microbe-Disease(Diet) interactions | |
| − | + | ||
| − | + | ||
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| − | *[http:// | + | |
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| − | + | ||
| − | + | ||
| − | + | - Metagenomic DB | |
| − | *[ | + | *[https://www.ebi.ac.uk/metagenomics/ MGnify] by EBI, UK |
| − | + | *[https://img.jgi.doe.gov/cgi-bin/m/main.cgi IMG] Integrated Microbial Genomes by Joint Genome Institute of DOE, US | |
| − | *[ | + | *[http://hmp2.org/ The integrative HMP] |
| − | + | ||
| − | *[http:// | + | |
| − | + | ||
| − | + | - Bacterial Culture Collection | |
| − | + | *[https://kctc.kribb.re.kr/kctc.aspx KCTC] Korean Collection for Type Cultures | |
| − | *[ | + | *[https://www.atcc.org/ ATCC Microbiology collection] |
| − | *[ | + | *[https://www.dsmz.de/ DSMZ] German Collection of Microorganisms |
| − | *[ | + | |
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| − | + | - Human Microbiome Bioactive Molecules (including Metabolites) DB & Analysis Tools | |
| − | *[ | + | *[https://www.microbiome-bioactives.org/ HMBR] THE HUMAN MICROBIOME BIOACTIVES RESOURCE |
| − | *[http:// | + | *[http://huttenhower.sph.harvard.edu/metawibele MetaWIBELE] A workflow to prioritize potentially bioactive gene products in microbial communities |
| − | *[http:// | + | *[http://huttenhower.sph.harvard.edu/macarron/ MACARRoN] A tool for systematic analysis of microbiome-associated metabolomes for identification of novel, potentially bioactive small moleculeshttps |
| − | == | + | - Mouse Diet Resource |
| − | - | + | *[https://researchdiets.com/ Research Diet] |
| − | *[http://www. | + | |
| − | + | == Proteome Resources == | |
| − | *[http://www. | + | - Human Proteome Database |
| − | *[http:// | + | *[http://www.humanproteomemap.org/ Human Proteome Map] 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues |
| − | - | + | *[https://www.proteomicsdb.org ProteomicsDB] >10,000 raw data files from 60 human tissues, 147 cell lines, and 13 body fluids |
| − | *[ | + | *[http://www.proteinatlas.org/ The Human Protein Atlas] The tissue-based map of human proteome based on Immunohistochemistry (for 32 different tissues and organs) |
| − | *[ | + | - Open stand-alone software for mass spectra database search (search engines) |
| + | *[http://www.marcottelab.org/index.php/MSblender MSblender] A combined search engine | ||
| + | *[http://proteomics.ucsd.edu/Software/MSGFDB/ MS-GFDB]: Its successor [http://proteomics.ucsd.edu/Software/MSGFPlus/ MS-GF+] is faster and more sensitive for high-resolution MS data. | ||
| + | *[http://www.thegpm.org/TANDEM/ X!TANDEM] | ||
| + | *[http://comet-ms.sourceforge.net/ Comet]: the direct descendant of [http://noble.gs.washington.edu/proj/crux/ Crux], which is an academic version of the commercial software SEQUEST | ||
| + | *[http://fenchurch.mc.vanderbilt.edu/software.php MyriMatch] | ||
| + | *[http://pubchem.ncbi.nlm.nih.gov/omssa/ OMSSA] Due to budgetary constraints NCBI has discontinued OMSSA. Historical binaries are available from here. | ||
| + | - Protein localization and Secretome DB | ||
| + | *[http://microvesicles.org/ Vesiclepedia] A DB for all types of Extracellular Vesicles (includes Exocarta) | ||
| + | *[http://www.exocarta.org/ Exocarta] A DB for Exosome | ||
| + | *[http://evpedia.info EVpedia] A DB for Extracellular Vesicles with many analysis software | ||
| + | |||
| + | == AI, Software == | ||
| + | - AI for Biomedicine | ||
| + | *[https://www.youtube.com/channel/UCtYLUTtgS3k1Fg4y5tAhLbw StatQuest] Excellent tutorial movies for learning machine learning and more (by Josh Starmer at UNC) | ||
| + | *[http://scikit-learn.org/ Scikit learn] Open software for Machine Learning | ||
*[https://www.coursera.org/course/ml?from_restricted_preview=1&course_id=971489&r=https%3A%2F%2Fclass.coursera.org%2Fml-004 Machine Learning by Andrew Ng] | *[https://www.coursera.org/course/ml?from_restricted_preview=1&course_id=971489&r=https%3A%2F%2Fclass.coursera.org%2Fml-004 Machine Learning by Andrew Ng] | ||
*[http://www-bcf.usc.edu/~gareth/ISL/ An Introduction To Statistical Learning] Free textbook and lecture notes | *[http://www-bcf.usc.edu/~gareth/ISL/ An Introduction To Statistical Learning] Free textbook and lecture notes | ||
| − | + | *[https://github.com/Jianing-Qiu/Awesome-Healthcare-Foundation-Models Foundation Models in Biomedicine] | |
| − | *[ | + | |
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| − | + | ||
| − | + | ||
| − | + | - Cool software | |
| + | *[https://cmdcolin.github.io/awesome-genome-visualization/?latest=true Awesome genome visualization] Genome visualization software depository | ||
*[http://revigo.irb.hr/ REVIGO] Visualize GO enrichment summary | *[http://revigo.irb.hr/ REVIGO] Visualize GO enrichment summary | ||
| + | *[https://gehlenborglab.shinyapps.io/upsetr/ UpSetR Shiny App] Visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries; R package is also available from [https://github.com/hms-dbmi/UpSetR github] | ||
*[http://bioinfogp.cnb.csic.es/tools/venny/ VENNY] Drawing Venn diagram | *[http://bioinfogp.cnb.csic.es/tools/venny/ VENNY] Drawing Venn diagram | ||
| + | |||
| + | == Other Resources == | ||
| + | - 특허 | ||
| + | *[https://ysis2.yonsei.ac.kr/ 연세대특허관리시스템] | ||
| + | *[https://www.ripis.or.kr/U_Ntis.do?method=m01 과제정보검색] by 정부R&D 특허성과관리시스템 | ||
| + | - Contract Research Organization (CRO) | ||
| + | *[https://www.bioneer.co.kr/20-s-2500.html Standard Protein Synthesis Service] by BIONEER | ||
| + | - IRB (Institutional Review Board, 의학연구윤리심의위원회) | ||
| + | *[https://irb.yonsei.ac.kr/ 연세e-IRB] | ||
| + | *[https://edu.kdca.go.kr/edu/index.html 질병관리청 IRB 교육사이트] | ||
| + | *[https://citiprogram.org CITI-program IRB education] | ||
| + | - Academic society & Research Center | ||
| + | *[http://www.ksbi.or.kr/ KSBI] Korean Society of Bioinformatics | ||
| + | *[http://www.ashg.org/ ASHG] American Society of Human Genetics | ||
| + | *[http://www.aacr.org AACR] American Association for Cancer Research | ||
| + | *[http://www.human-microbiome.org/ IHMC] The International Human Microbiome Consortium | ||
| + | *[http://www.cancer.or.kr KCA] Korean Cancer Association | ||
| + | *[http://www.kogo.or.kr KOGO] Korea Genome Organization | ||
| + | *[http://www.ksmcb.or.kr/ KSMCB] Korean Society of Molecular and Cellular Biology | ||
| + | *[http://new.ksbmb.or.kr/ KSBMB] Korean Society of Biochemistry and Molecular Biology | ||
| + | *[http://www.kormb.or.kr/ KMB] The Korean Society of Microbiology and Biotechnology | ||
| + | *[http://www.msk.or.kr/msk/ MSK] The Microbiological Society of Korea | ||
| + | *[http://mrc-systemsmed.org/ Yonsei Medical Research Center for Systems Medicine] | ||
| + | |||
| + | - Cancer Immunology Biotech company | ||
| + | *[https://gv20oncotherapy.com/ GV20] AI-based cancer immunotherapy development | ||
| + | *[https://fortugabio.com/ FortugaBio] Cancer Immunotherapy | ||
| + | *[http://www.eutilex.com/ Eutilex] Cancer Immunotherapy | ||
| + | |||
| + | - Microbiome Biotech company | ||
| + | *[https://microba.com/ MICROBA] Precision microbiome profiling and drug discovery | ||
| + | *[https://microbiotica.com/ Microbiotica] Microbiome-based therapeutics and biomarker discovery | ||
| + | *[https://clinical-microbiomics.com/ Clinical Microbiomics] offer expert microbiome analysis for clinical, pre-clinical studies | ||
| + | *[http://www.enterome.fr/ Enterome] Microbiome analysis for healthcare and drug development | ||
| + | *[http://www.secondgenome.com/ Second Genome] Microbiome company | ||
| + | *[http://www.serestherapeutics.com/ Seres Health] Microbiome company | ||
| + | *[http://www.vedantabio.com/ Vedanta Biosciences] Microbiome company | ||
| + | *[https://www.hempharma.bio/ HEM Pharma] | ||
| + | |||
| + | - Precision Medicine Biotech company | ||
| + | *[https://celsiustx.com/ Celsius Terapeutics] Novel targets and biomarker identified through single-cell RNA sequencing analysis | ||
| + | *[http://www.humanlongevity.com/ Human Longevity Inc.] | ||
| + | *[http://www.personalis.com/ Pesonalis] Genome-guided Medicine | ||
| + | *[http://www.calicolabs.com/ Calico] Aging-related disease research company | ||
| + | *[https://bostongene.com/ BostonGene] Tumor Portrait technology for Precision Oncology | ||
| + | |||
| + | - Others | ||
| + | *[https://dna.macrogen.com/ Macrogen] | ||
| + | *[http://www.tedmed.com/ TEDMED] TEDTALK for Medicine and healthcare problems | ||
| + | *[http://retractionwatch.com/ Retraction watch] | ||
| + | *[https://thevc.kr/] TheVC | ||
Latest revision as of 20:23, 8 July 2024
[edit] Google DataSet Search Engine
[edit] Gene/Genome Annotations
- CCDS The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation
- GENCODE The Encyclopedia of Genes
- Metasape Gene annotation and Enrichment analysis resource by NIH
[edit] Variome Resources
- Variation DBs
- ExAC (Exome Aggregation Consortium) Exome variation data from >60k individuals
- 1000 Genome Project Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations
- UK10K Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England
- Genomics England Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer.
- DiscovEHR Collaboration between the Regeneron Genetics Center (WES) and Geisinger Health System (EHR) provides the vcf by 50,000 MyCode participants
- European Variation Archive Most comprehensive and organized by studies (include Clinical variants)
- NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
- iJGVD Integrative Japanese Genome Variation Database
- HGV Database The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
- Functional significance of variants
- Eigen Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
- CADD: Combined Annotation Dependent Depletion a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
- GWAVA: Genome Wide Annotation of VAriants a tool which aims to predict the functional impact of non-coding genetic variants (human only, supervised integration)
- VEP Variant Effect Predictor by EBI (very easy to install and use)
- Condel Variant effect score by integration of SIFT, Polyphen2, Massessor, MAPP, Logre
- SIFT(Sorting Intolerent from Tolerent substitution)
- SIFT4G SIFT for many genomes
- PolyPhen-2 (Polymorphism Phenotyping v2) for human coding region only
- RegulomeDB Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab)
- HaplogReg Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
[edit] Phenome/Diseasome Resources
- Human Disease DBs
- DisGeNET MetaDB for disease genes and variants (very comprehensive and open license)
- Open Targets Another very comprehensive DB for disease target (mostly protein-coding genes) and related evidence
- denovo-db a compendium of human de novo variants
- DISEASES gene-disease association from text mining (GHR, Uniprot, textmining)
- GHR Genetics Home Reference (by NCBI)
- Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
- Human Phenotype Ontology
- OMIM Human disease DB (needs License to distribute)
- OrphaData Open database for rare diseases and orphan drug (by Orphanet)
- GAD Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
- UMLS Unified Medical Language Systems
- ICD International Classification of Disease by WHO
- DGA Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
- GenomeRNAi v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets
- OGEE Online GEne Essentiality database
- Human-Mouse Disease Connection a part of MGI
- QTL depositories
- GTEx Portal eQTL for ~50 different tissue types in humans
- GWAS resources
- COVID-19 Host Genetics InititativeCOVID-19 GWAS regulsts
- GWAS ATLAS Atlas of GWAS Summary Statistics (most comprehensive!)
- GWAS catalog Disease-associated variants; Now providing GWAS summary stat data
- GeneATLAS GWAS for ~780 traits using 452,264 UK Biobank White British individuals
- PheGenI Phenotype-Genotype Integrator: For a query trait, it return GWAS loci collected from all available data resources (very convenient to make a single GWAS data set for each trait)
- LDHUB a centralized database of summary-level GWAS results
- Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP) Better than GWAS catalog, including eQTL,QTLs
- GWASdb includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
- DistiLD Diseases and Traits in Linkage Disequilibrium Blocks
- Genotype raw data depositories
- Human Functional Genomics Project Raw data are available from BBMRI-NL data infrastructure
- UK Biobank Genotype and extensive phenotype data for ~500k UK people
- European Genome-phenome Archive(EGA) Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis
- dbGaP The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
- Clinical/Disease variant databases
- CGD Clinical Genomic Database
- HGMD The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
- OMIM Germline mutations for genetic diseases
- Roche Cancer Genome Database (RCGDB) Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
- IDbase Human Immunodeficiency-causing mutation database
- NCBI ClinVar human variations and their relations to the human health (Not includes unreviewed data from GWAS)
- Others
- COGS nature resources CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
- Personal Genome Project
- DECIPHER Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)
[edit] Interactome, Pathway/Signature Resources
- Interactome DBs
- iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI, Reactome, VirHostnet, and QuickGO.
- STRING Known and predicted PPI
- Human Reference Interactome Project Y2H-based human protein interactions
- Pathway DBs
- Pathguide.org A very comprehensive list of pathway and network databases
- Gene Ontology by Gene Ontology Consortium
- KEGG pathways and many more
- Biocyc includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc
- Reactome A manually curated and peer-reviewed pathway DB
- Pathway Interaction Database (PID) Human pathways curated by NCI-Nature/imported from BioCarta/Reactome
- CORUM Comprehensive Resource of Mammalian Protein Complexes
- NetPath A database for signaling pathways (cancer/immune signaling pathways)
- SIGNOR 11000 manually-annotated causal relationships between proteins that participate in signal transduction
- UniProt-GOA by EBI (support multi-species annotation)
- UniPathway a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)
- Signature Gene Set DBs
- MsigDB License required for redistribution
- GeneSigDB Manually curated gene sets from Pubmed literature
- ImmnuneSigDB Compendium of immune signatures (now available from MsigDB)
- CancerSEA which provides 14 signature profiles for characterization of cancer cells
- DSigDB Drug signature database for gene set analysis
- L1000CDS2 Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
- CREEDS CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method
[edit] Regulome Resources
- TF and motif DB
- The Human Transcription Factors 2765 putative TFs and 1639 confident TFs by manual curation
- CIS-BP (Catalog of Inferred Sequence Binding Preferences) >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as HOCOMOCO JASPAR UNIPROBE TRANSFAC
- Epigenomics Consortium projects
- ENCODE Encyclopedia of DNA Elements project portal
- Road map Epigenomics NIH Roda map Epigenomics project home
- International Human Epigenome Consortium (IHEC) The umbrella organization for international epigenomic efforts
- 4D Nucleome To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)
- Promoter DB
- EPD Eukaryotic Promoter Database; Databases of experimentally validated (by either publication or in-house assay) promoters in various organisms
- Enhancer DB
- Enhancer Atlas Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues)
- dbSUPER contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
- HEDD Human Enhancer Disease Database (~2.8M enhancers from ENCODE, FANTOM5, RoadMap and annotations for disease, target, variant, conservation)
- DiseaseEnhancer manual curation of disease-associated enhancers
- Transcriptional Start Site (TSS) DB
- DBTTS contains 491 million TSS tag sequences for 20 tissues and 7 cell cultures in human and mouse
- Chip-seq/DNase-seq DB
- Cistrome DB the most comprehensive DB for Chip-seq and DNase-seq data
- Enhancer-Promoter Interaction DB
- JEME Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines
- microRNA list and expression atlas
- miRBase miRNA database by Manchester University
- microRNA.org download miRNA expression atlas for human, mouse, rat
- microRNAome microRNA RNA-seq based atlas for 46 primary cell types and 42 cancer or immortalized cell lines
- microRNA-target links (Gold standard)
- miRWalk2.0 Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
- miRTarBase Experimental-based microRNA-target links (most popular)
- microRNA-disease
- Human microRNA Disease Database(HMDD) Manually curated microRNA-disease links (most comprehensive)
- PhenomiR DB for dysregulated miRNA in diseases
- dbDEMC DB for dysregulated miRNA in Cancer
- miRGator data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...
- miRNA Target predictions
- mirDIP >150M human miRNA-target predictions collected from 30 resources with integrative score
- CLIP-seq database
- StarBase DB for CLIP-seq data
- lncRNA Resources
- FANTOM-CAT An atlas of human long non-coding RNAs with accurate 5' ends
- NONCODE Integrative annotation of long noncoding RNAs
- lncRNAdb a reference DB for long noncoding RNAs
- RAIN RNA–protein Association and Interaction Networks Intro to RAIN
- NPInter ncRNA interaction database (ncRNA and other molecules)
- RAID RNA-associated interaction DB (very comprehensive)
- LncRNADisease a DB for lncRNA associated diseases
- ncFANs a web server for functional annotation of ncRNA
- LincSNP a DB of disease-associated SNP in human lncRNA and their TFBS
- POSTAR a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)
[edit] Single Cell Analysis Resources
- Spatial Omics Resources
- Human Cell Atlas
- HCA
- Chan Zukerburg Initiative HCA seed networks
- COVID-19 Cell Atlas Data portal by HCA
- scRNA-seq data analysis resources
- Seurat The package for scRNA-seq data analysis
- Velocyto RNA Velocity analysis with steady-state model
- scVelo Generalized RNA Velocity analysis through dynamic modeling
- scRNA-seq analysis course by Sanger
- CellPhoneDB A repository of curated receptors, ligands and their interactions.
- Awesome single cell
- scRNA-tools DB
- Depositories for scRNA-seq data
- Single Cell Portal scRNA-seq database by Broad Institute
- scRNASeqDB scRNA-seq database by UTHSC
- conquer A repository of consistently processed, analysis-ready single-cell RNA-seq data sets
- Jinglebells A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
- SCPortalen human and mouse single-cell centric database
- 10X Genomics Datasets by 10X Genomics
[edit] Chemical Biology and Drug Research Resources
- Prioritizing Drugs for target gene regulation
- Drug Gene Budger based on LINCS, GEO, CMAP data DGB reference
- Drug and Bioactive chemical DBs
- Drug Repurposing Hub a best-in-class drug screening collection of >3,000 clinical drugs and their annotation (structure, MoA, protein targets)
- Drugable.com by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
- PubChem A DB contains drug structure and function by NCBI
- ChEMBL A DB contains drug structure and functions by EBI
- Drugs@FDA A DB for FDA approved drugs
- DailyMed High quality Information about marketed drugs by NCBI
- SuperDrug A DB contains 3D-structures of drugs
- Clinical Trial Information
- ClinicalTrials.gov DB for clinical trials conducted around the world
- Drug Target DBs
- DGIdb An integrated Drug-Gene Interaction DB
- A curated drug-target map by curation of ChEMBL database, DrugCentral database, canSAR knowledge base (Gold Standard drug-target)
- KEGG DRUG contains information about only approved drugs
- STITCH DB for known and predicted chemical-protein interaction
- Drugbank A major DB of drug/target
- Therapeutic Target Database (TTD) A major DB of drug/target
- MATADOR Manually Annotated Targets and Drugs Online Resource
- IUPHAR/BPS Guide to Pharmacology A DB of in-depth information of drug targets and ligands
- PDSP Ki DB data warehouse for published and internally-derived Ki, or affinity of drugs at targets
- Drug signature, Pharmacogenomics, Toxicogenomics DBs
- DSigDB Drug signature database for gene set analysis
- CLUE The expanded CMap including 1.3M L1000 profiles for 27,927 perturbagens (476,251 expressions)
- iLINCS Integrated System to Analyze LINCS and other data
- Connectivity Map (CMap) 7,000 expression profiles representing 1,309 compounds
- The Comparative Toxicogenomics database(CTD) The major DB of chemical-disease links from literature curation
- TG-GATE Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans
- Chemical Effects in Biological Systems(CEBS) an integrated public repository for toxicogenomics data
- PharmGKB The Parmacogenomics Knowledgebase
- SIDER Side Effect Resource
- Drug-Gene Interaction DBs
- MOSAIC Chemical-genetic interactions in Yeast (cover >13000 compounds)
[edit] Cancer Biology Resources
- Cancer Somatic Mutations DBs
- meta-knowledgebase of somatic variants Harmonized integration of Cancer Genome Interpreter, CIVIC, JAX-CKB, MolecularMatch, OncoKB, PMKB
- COSMIC(The Catalog Of Somatic Mutations In Cancer) By Sanger with expert curation
- DoCM A database of functional variants validated in cancer
- CIViC A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
- Cancer Somatic Mutation Visualization
- Proteinpaint Exploring genomic alteration in pediatric cancer
- Cancer Gene DBs
- CGC(Cancer Gene Census} A catalog of genes with mutations that are causally implicated in cancer (by COSMIC)
- 125 mutation-based drivers see Supple TableS2A (71 TSG and 54 OG by 20/20 rule)
- TSGene Literature-curated 1217 human TSGs (1018 protein-coding and 199 non-coding genes) and 320 protein-coding oncogenes
- CCGD(Candidate Cancer Gene Database)A database of cancer driver genes from transposon-based forward genetic screens in mice
- 77 Cancer Genes by amplification and overexpression see Supple TableS2
- NCG(The Network of Cancer Genes) (~500) CGC + (~1000) Candidate genes from Panel Seq, WES, WGS studies
- Cancer Genomics Research Gateway
- NCI Genomic Data Commons GDC provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies.
- ICGC data portal raw data from ICGC and TCGA
- TARGET(Therapeutically Applicable Research To Generate Effective Treatments) Childhood Cancer Genome Project by NCI
- PedPanCan(A Pan-Cancer Study of Childhood Cancers) by Multi-Institutes including St. Jude Children's Research Hospital
- NCI Office of Cancer Genomics OCG is dedicated to supporting cancer genomics research by sharing molecular data from its programs to enhance understanding of cancer.
- CTD2 data portal Data Portal of Cancer Target Discovery and Development program which strives to functionally validate discoveries from large-scale genomic initiatives.
- Synapse GENIE The largest public cancer genome data by ACCR (see ACCR GENIE project)
- Cancer Program Resource Gateway by Broad
- Cancer Genomics Data Analysis Cloud Platforms
- UCSC Xena An online exploration tool for public (TCGA, ICGC and more) and private, multi-omic and clinical/phenotype data
- ISB-CGC Cancer Genomics Cloud by ISB
- WebMeV Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).
- Tumor Microenvironment Analysis tools
- TIMER Web server for a comprehensive TME analysis
- xCell Tumor cellular heterogeneity analysis web server; R package is also available from github
- Cancer Pharmacogenomics
- PharmacoDB Integrative database for cancer pharmacogenomics (CCLE, GDSC, CTRP, and more)
- CTRP The Cancer Therapeutics Response Portal (~550 drugs x ~890 cell lines)
- Genomics of Drug Sensitivity in Cancer (GDSC) (~250 drugs x ~1110 cell lines)
- Cancer Cell line Encyclopedia (CCLE) (~20 drugs x ~1060 cell lines)
- Cancer cell essential genes
- GenomeCRISPR A database for high-throughput CRISPR/Cas9 screening experiments
- Achilles Project shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8)
- COLT-cancer database shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines
[edit] Immunogenetics DBs and tools
- Immune Epitope Database The most comprehensive (immunogenic and pathogenic) epitope database
- TANTIGEN Tumor T-cell Antigen database (>1000 peptides by literature curation)
- Cancer Antigenic Peptide Database ~400 peptides by literature curation
[edit] Microbiomics DBs and tools
- Gut microbial biobank by Automated culturomics
- [1] CAMII biobank
- Microbiome Data Analysis Resources
- Microbiome Discovery Awesome Lectures by Dan Knight
- Huttenhower Lab A great resource for analysis tools
- Harvard Chan Microbiome in Public Health Center (HCMPH)
- Microbiome Catalogs and Taxonomy
- GTDB BACTERIAL GENOME TAXONOMY DATABASE
- HRGM Human Reference Gut Microbiome by Yonsei University
- UHGG Unified Human Gastrointestinal Genome by EBI
- GMGC Global Microbial Gene Catalog by EMBL
-Microbiome-Disease(drug, diet) interaction DBs
- Disbiome Microbe-Disease interactions
- MASI Microbe-Drug(Disease, Diet) interactions
- gutMDisorder Microbe-Disease(Diet) interactions
- Metagenomic DB
- MGnify by EBI, UK
- IMG Integrated Microbial Genomes by Joint Genome Institute of DOE, US
- The integrative HMP
- Bacterial Culture Collection
- KCTC Korean Collection for Type Cultures
- ATCC Microbiology collection
- DSMZ German Collection of Microorganisms
- Human Microbiome Bioactive Molecules (including Metabolites) DB & Analysis Tools
- HMBR THE HUMAN MICROBIOME BIOACTIVES RESOURCE
- MetaWIBELE A workflow to prioritize potentially bioactive gene products in microbial communities
- MACARRoN A tool for systematic analysis of microbiome-associated metabolomes for identification of novel, potentially bioactive small moleculeshttps
- Mouse Diet Resource
[edit] Proteome Resources
- Human Proteome Database
- Human Proteome Map 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
- ProteomicsDB >10,000 raw data files from 60 human tissues, 147 cell lines, and 13 body fluids
- The Human Protein Atlas The tissue-based map of human proteome based on Immunohistochemistry (for 32 different tissues and organs)
- Open stand-alone software for mass spectra database search (search engines)
- MSblender A combined search engine
- MS-GFDB: Its successor MS-GF+ is faster and more sensitive for high-resolution MS data.
- X!TANDEM
- Comet: the direct descendant of Crux, which is an academic version of the commercial software SEQUEST
- MyriMatch
- OMSSA Due to budgetary constraints NCBI has discontinued OMSSA. Historical binaries are available from here.
- Protein localization and Secretome DB
- Vesiclepedia A DB for all types of Extracellular Vesicles (includes Exocarta)
- Exocarta A DB for Exosome
- EVpedia A DB for Extracellular Vesicles with many analysis software
[edit] AI, Software
- AI for Biomedicine
- StatQuest Excellent tutorial movies for learning machine learning and more (by Josh Starmer at UNC)
- Scikit learn Open software for Machine Learning
- Machine Learning by Andrew Ng
- An Introduction To Statistical Learning Free textbook and lecture notes
- Foundation Models in Biomedicine
- Cool software
- Awesome genome visualization Genome visualization software depository
- REVIGO Visualize GO enrichment summary
- UpSetR Shiny App Visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries; R package is also available from github
- VENNY Drawing Venn diagram
[edit] Other Resources
- 특허
- 연세대특허관리시스템
- 과제정보검색 by 정부R&D 특허성과관리시스템
- Contract Research Organization (CRO)
- Standard Protein Synthesis Service by BIONEER
- IRB (Institutional Review Board, 의학연구윤리심의위원회)
- Academic society & Research Center
- KSBI Korean Society of Bioinformatics
- ASHG American Society of Human Genetics
- AACR American Association for Cancer Research
- IHMC The International Human Microbiome Consortium
- KCA Korean Cancer Association
- KOGO Korea Genome Organization
- KSMCB Korean Society of Molecular and Cellular Biology
- KSBMB Korean Society of Biochemistry and Molecular Biology
- KMB The Korean Society of Microbiology and Biotechnology
- MSK The Microbiological Society of Korea
- Yonsei Medical Research Center for Systems Medicine
- Cancer Immunology Biotech company
- GV20 AI-based cancer immunotherapy development
- FortugaBio Cancer Immunotherapy
- Eutilex Cancer Immunotherapy
- Microbiome Biotech company
- MICROBA Precision microbiome profiling and drug discovery
- Microbiotica Microbiome-based therapeutics and biomarker discovery
- Clinical Microbiomics offer expert microbiome analysis for clinical, pre-clinical studies
- Enterome Microbiome analysis for healthcare and drug development
- Second Genome Microbiome company
- Seres Health Microbiome company
- Vedanta Biosciences Microbiome company
- HEM Pharma
- Precision Medicine Biotech company
- Celsius Terapeutics Novel targets and biomarker identified through single-cell RNA sequencing analysis
- Human Longevity Inc.
- Pesonalis Genome-guided Medicine
- Calico Aging-related disease research company
- BostonGene Tumor Portrait technology for Precision Oncology
- Others
- Macrogen
- TEDMED TEDTALK for Medicine and healthcare problems
- Retraction watch
- [2] TheVC
