本列表收录了全球生物医学数据中心、物种参考基因组及基因组注释库、TCGA/ICGC癌症基因组、非编码RNA与转录调控、免疫组学、基因突变、多组学整合数据库以及单细胞转录组等专业领域的医学数据库平台。
- 🗄️ 综合数据中心 (Data Centers)
- 📖 基因组参考物种与注释 (Reference Genomes)
- 🎗️ TCGA 癌症基因组数据库 (TCGA)
- 🎗️ ICGC 国际癌症基因组联盟 (ICGC)
- 🔗 多组学整合数据库 (Merged Databases)
- 🧬 非编码与转录调控 (ENCODE & Non-coding)
- 🛡️ 免疫学数据库 (Immunology Databases)
- 🧬 突变与变异数据库 (Mutation Databases)
- 📈 基因表达与转录调控 (Expression Databases)
- 🔬 蛋白质与相互作用 (Protein & Interaction Databases)
- 🧪 细胞系与药物反应 (Cell Line & Drug Response)
- 🧫 单细胞转录组数据库 (Single Cell Databases)
- 🛠️ 在线分析工具与服务 (Online Analysis Tools)
- 🎗️ 癌症相关基因数据库 (Cancer Genes)
- 🏥 临床试验与队列 data (Clinical Trials & Cohorts)
- 🧬 甲基化与表观遗传数据库 (Methylation & Epigenetics)
- 🦠 病毒基因组数据库 (Virus Databases)
- 🌿 中医药与天然产物数据库 (TCM Databases)
- 🧬 ecDNA 染色体外DNA数据库 (ecDNA Databases)
- 🛡️ 肿瘤免疫治疗数据集 (Immunotherapy Datasets)
- 🧠 领域专家知识库 (Knowledgebases)
- 🖼️ 医学影像数据库 (Medical Image Datasets)
- 🌐 重大国际科学项目 (Large-scale Science Projects)
- 🏷️ 基因与功能注释库 (Annotation Databases)
- ⚡ 扰动与基因编辑数据集 (Perturbation Datasets)
- 📦 数据下载与接口工具包 (Data Download Utilities)
- awesomedata/awesome-public-datasets: A topic-centric list of HQ open datasets. PR ☛☛☛
- CDE Browser|NCBI项目查询
- CNGBdb - 国家基因库生命大数据平台
- Database Summary Paper Categories
- DaTo | Search
- EGA European Genome-Phenome Archive
- ELIXIR Core Data Resources | ELIXIR
- Genome Sequence Archive
- Genome Sequence Archive for Human
- Home - Data Commons
- Home - Database Commons
- Human cancer databases (Review)
- List of Current Global Core Biodata Resources - Global Biodata Coalition
- MetaSRA
- NCI Human Tumor Atlas Network
- OmicsDI
- ORCESTRA
- Run Selector :: NCBI
- SIB Swiss Institute of Bioinformatics | Expasy
- SRA Explorer
- StatsUpAI
- TCGA Computational Tools - NCI
- 国家生物信息中心国家生物信息中心
- 1000 Genomes | A Deep Catalog of Human Genetic Variation
- AstraZeneca-NGS/reference_data: Reference data: BED files, genes, transcripts, variations.
- AWS iGenomes
- BioKA
- CancerStop
- Codon Usage Database
- CPC
- Ensembl Genome Browser
- Ensembl genome browser 91
- excluderanges - Google 云端硬盘
- Exome Aggregation Consortium
- GDC参考文件
- GENCODE
- Gene Ontology Resource
- Genekitr
- ggd consists of: — GGD
- gnomAD
- GSEA
- GWAS一些注释数据
- Home | Alliance of Genome Resources
- Human Genome Reference Consortium
- iGenomes
- marbl/CHM13: The complete sequence of a human genome
- MGI-Mouse Genome Informatics-The international database resource for the laboratory mouse
- OMIM - Online Mendelian Inheritance in Man
- Overview - Quartet Data Portal
- Rat Genome Database - Home
- Refgenie
- TeloBase
- UK Biobank
- Broad GDAC Firehose
- GDC 数据字典
- GEPIA (Gene Expression Profiling Interactive Analysis)
- MEXPRESS
- TCGA Fusion Gene Database
- TCIA Collections
- ualcan.path.uab.edu/home
- UCSC TumorMap
- Chromoscope PCAWG
- ICGC ARGO | Homepage
- ICGC Data Portal
- PCAWG datasets
- 转移瘤https://database.hartwigmedicalfoundation.nl
- cBioPortal/datahub: A centralized location for storing curated data ready for inclusion in cBioPortal.
- iSMOD
- opencb/cellbase: High-Performance NoSQL database and RESTful web services to access to most relevant biological data
- PeCan | St. Jude Cloud
- Synapse | Sage Bionetworks
- UCSC Xena
- Welcome — China Kadoorie Biobank (CKB)
- CATlas
- CenhANCER
- circatlas.biols.ac.cn
- CircNet
- ENCODE: Encyclopedia of DNA Elements – ENCODE
- GtRNAdb: Genomic tRNA Database
- miRBase
- RM2Target | A comprehensive database for the target genes of WERs of RNA modifications
- SCREEN: Search Candidate Regulatory Elements by ENCODE
- SilencerDB
- Welcome to IHEC · IHEC
- 1000 Immunomes Project | 1000 Immunomes Project | Stanford Medicine
- 2018-12-07 PD-1 approval timeline | Tableau Public
- Antigen data | Immunoinformatics analysis - omicX
- CAMOIP
- CEDAR - Cancer Epitope Database and Analysis Resource
- CRI iAtlas
- Databases for immunoinformatics - omicX
- DeepNeo web
- Discovering Dominant Tumor Immune Archetypes in A Pan-Cancer Census | The UCSF Data Library
- Human Immunome Project | A New Model for Global Health
- ICBatlas
- ICRAFT
- IEDB.org: Free epitope database and prediction resource
- IMGT®, the international ImMunoGeneTics information system®
- ImmPort Shared Data
- Immune Repertoire | VisualizIRR
- Immunological Genome Project
- InnateDB: Systems Biology of the Innate Immune Response
- Interaction plots
- IOExplorer
- Neodb
- PISNO-snoRNA-ICB
- PRECOG - Prediction of clinical outcomes from genomics
- PredictIO
- TCIA
- TCRdb
- The Cancer Imaging Archive (TCIA)
- TIMEDB
- TIP|捕获癌症免疫表型
- TISIDB
- TISMO
- TSNAdb
- Tumor Immune Dysfunction and Exclusion (TIDE)
- VDJdb
- COSMIC | Catalogue of Somatic Mutations in Cancer
- GENIE - syn7222066 - Wiki
- Impact of Genomic Variation on Function (IGVF) Consortium
- LitVar - NCBI - NLM - NIH
- OncoKB™ - MSK's Precision Oncology Knowledge Base
- seandavi/awesome-cancer-variant-databases: A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
- The ChangKang Project
- ARCHS4
- Bgee: gene expression data in animals
- Carcinoma EcoTyper
- Digital Expression Explorer 2
- EcoTyper
- Home - Gene Expression Nebulas - Gene Expression Nebulas
- Home < Expression Atlas < EMBL-EBI
- Home | Gemma
- MiPanda
- recount3: uniformly processed RNA-seq
- Search for harmonized transcriptome data - refine.bio
- AlphaFold Protein Structure Database
- DongqiFu/DPPIN: DPPIN: A Biological Dataset of Dynamic Protein-Protein Interaction Networks, Preprint.
- iProX - integrated Proteome resources
- OpenCell
- Pfam: Home page
- ProteomeXchange Datasets
- Proteomic Data Commons
- STRING: functional protein association networks
- The Human Protein Atlas
- UniProt
- [clue.io] ConnectivityMap
- Broad Institute Cancer Cell Line Encyclopedia (CCLE)
- Cancer Therapeutics Response Portal
- Cell Model Passports
- CPIC
- ctr-db
- DepMap: The Cancer Dependency Map Project at Broad Institute
- DrugBank Online | Database for Drug and Drug Target Info
- FAERS Quarterly Data Extract Files
- FDA Adverse Event Reporting System (FAERS): Latest Quarterly Data Files | FDA
- GEMICCL : Gene Expression and Mutation In Cancer Cell Line
- Home page - Cancerrxgene - Genomics of Drug Sensitivity in Cancer
- Home | PharmacoDB
- SEARCH
- www.dgidb.org
- ACT
- Cancer B cell blueprint
- CellChat
- CellKnowledge
- CellMarker
- CellMarker2.0
- CellO Viewer
- cellphonedb.org
- CellResDB
- CellTypist | automated cell type annotation for scRNA-seq datasets
- Cross-tissue Immune Cell Atlas
- CROST
- Curated Cancer Cell Atlas
- CZ CELLxGENE Discover - Cellular Visualization Tool
- CZ CELLxGENE Discover Census — cellxgene-census
- DISCO
- Gastric cancer
- Geno Graphix
- HBCA | Data Access
- HCA Data Portal
- hECA
- Home - Cancer Single-cell Expression Map - CNCB-NGDC
- Home - Cell Taxonomy - CNCB-NGDC
- ImmCluster
- kana
- Mapping the developing human immune system across organs | Human Developmental Cell Atlas
- MOSAIC is the world’s largest spatial multiomics dataset in oncology
- PanglaoDB - A Single Cell Sequencing Resource For Gene Expression Data
- Single Cell Portal
- Spatial Transcript Omics DataBase - STOMICS DataBase - 空间转录组学数据库
- T cell map
- Tahoe | Previously Vevo Therapeutics
- TF-Marker
- TIGER: Tumor Immunotherapy Gene Expression Resource
- TISCH
- 细胞标记物智能查询系统
- Bionimbus PDC Datasets
- CGI:鉴定肿瘤变异
- Enrichr
- g:Profiler – a web server for functional enrichment analysis and conversions of gene lists
- Galaxy
- Galaxy Community Hub
- GEPIA 2
- HBICloud
- HiOmics
- Home - Reactome Pathway Database
- https://proteinpaint.stjude.org
- IGV
- ImmuCellAI
- Immune Dictionary App - Default
- Introduction - MEME Suite
- Introduction to Circos, Features and Uses // CIRCOS Circular Genome Data Visualization
- Logistic Regression-based Immunotherapy-response Score
- Metascape
- MiPanda|基因NGS分析
- Multi-Gene Survival Analysis
- Nucleome
- OncoLnc
- PCAWG Passenger Mutation Analysis
- SigCom LINCS
- TANRIC: Home
- Welcome to ToppGene
- 临床生信之家
- Bushman Lab: Genelists
- IntOGen - Cancer Mutations Browser
- ONGene
- Tumor suppressor gene database (TSGene) Home
- Keynote • Keynote Clinical Trials
- Keynote • Lung Keynote Oncology Clinical Trials
- Vivli - Center for Global Clinical Research Data
- cytocelldb.unc.edu
- eccDNA Atlas-Home
- eccDNAdb
- Home | AmpliconRepository
- Mitelman Database Chromosome Aberrations and Gene Fusions in Cancer
- carmonalab/SignatuR: A database of useful gene signatures for single-cell analysis
- ICGC ARGO Docs
- igordot/babelgene
- Organism.dplyr
- stephenturner/annotables: R data package for annotating/converting Gene IDs
- Variant Annotators | OncoKB™ API
- Viewer - GDC Docs
- ankane/dbx: A fast, easy-to-use database library for R
- Apache Arrow | Apache Arrow
- arrow/r at master · apache/arrow
- Bioconductor - biomaRt
- Bioconductor - simona
- Bioconductor/GenomicDataCommons: Provide R access to the NCI Genomic Data Commons portal.
- BioOmics/iSeq: Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
- CRAN - Package dbplyr
- Databases using R
- EGA-archive/ega-download-client: A basic Python-based EGA download client
- icgc/icgc-get: Universal download client for ICGC data residing in various environments
- karissawhiting/cbioportalR: R package to wrap cBioPortal's API to pull data from public or private cBioPortal databases
- openbiox/bget: Lightweight downloader for bioinformatics data, databases and files. Golang http library, wget, curl, axel, git, and rsync were used as the download engine.
- pachterlab/ffq: A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.
- r-lib/vroom: Fast reading of delimited files
- rpetit3/fastq-dl: Download FASTQ files from SRA or ENA repositories.
- RTCGA
- RTCGAToolbox
- rvalieris/parallel-fastq-dump: parallel fastq-dump wrapper
- Sage-Bionetworks/synapsePythonClient: Programmatic interface to Synapse services for Python
- Sage-Bionetworks/synapser: An R package providing programmatic access to Synapse
- Sequence Retrieval
- Synapse Python Client documentation — Synapse Python Client 1.8.1
- The GenomicDataCommons Package